Trinity Assembly

Asrix · February 2, 2022, 10:39pm

I don’t understand the error I am getting.

For the bug report it says that

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2 .
Fatal error: Exit code 2 ()

With the claim that the tool was executed with one or more duplicate input datasets. I only have one copy of each of my input files in my Galaxy data and they are the only two files I have.

The standard tool output also doesn’t have an obvious error (had to trim to make it under the character limit):

Trinity-v2.9.1
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------

------------ In silico Read Normalization ---------------------
– (Removing Excess Reads Beyond 200 Coverage –

running normalization on reads: $VAR1 = [
      [
        '/local/tmp.nAn32TYA8x/left_input0.fastqsanger.gz'
      ],
      [
        '/local/tmp.nAn32TYA8x/right_input0.fastqsanger.gz'
      ]
    ];
Tuesday, February 1, 2022: 14:05:55 CMD: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 247G --max_cov 200 --min_cov 2 --CPU 64 --output /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization --max_CV 10000 --left /local/tmp.nAn32TYA8x/left_input0.fastqsanger.gz --right /local/tmp.nAn32TYA8x/right_input0.fastqsanger.gz --pairs_together --PARALLEL_STATS
-prepping seqs
Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /local/tmp.nAn32TYA8x/left_input0.fastqsanger.gz) >> left.fa
CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /local/tmp.nAn32TYA8x/right_input0.fastqsanger.gz) >> right.fa
CMD finished (112 seconds)
CMD finished (113 seconds)
CMD: touch left.fa.ok
CMD finished (0 seconds)
CMD: touch right.fa.ok
CMD finished (0 seconds)
Done converting input files.CMD: cat left.fa right.fa > both.fa
CMD finished (8 seconds)
CMD: touch both.fa.ok
CMD finished (0 seconds)
-kmer counting.

----------- Jellyfish --------------------
– (building a k-mer catalog from reads) –

…
done parsing 543378591 Kmers, 543378591 added, taking 846 seconds.

done parsing 543378591 Kmers, 543378591 added, taking 871 seconds.
STATS_GENERATION_TIME: 877 seconds.
STATS_GENERATION_TIME: 895 seconds.
CMD finished (1811 seconds)
CMD finished (1863 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/bin/sort --parallel=64 -k1,1 -T . -S 123G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/bin/sort --parallel=64 -k1,1 -T . -S 123G >> right.fa.K25.stats.sort
CMD finished (16 seconds)
CMD finished (17 seconds)
CMD: touch left.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.sort.ok
CMD finished (0 seconds)
-defining normalized reads
CMD: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/opt/trinity-2.9.1/util/…//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
-opening left.fa.K25.stats.sort
-opening right.fa.K25.stats.sort
-done opening files.
CMD finished (785 seconds)
CMD: touch pairs.K25.stats.ok
CMD finished (0 seconds)
CMD: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/opt/trinity-2.9.1/util/…//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 2 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
60026299 / 61844565 = 97.06% reads selected during normalization.
0 / 61844565 = 0.00% reads discarded as likely aberrant based on coverage profiles.
545695 / 61844565 = 0.88% reads discarded as below minimum coverage threshold=2
CMD finished (509 seconds)
CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
CMD finished (0 seconds)
-search and capture.
-preparing to extract selected reads from: /local/tmp.nAn32TYA8x/right_input0.fastqsanger.gz … done prepping, now search and capture.
-capturing normalized reads from: /local/tmp.nAn32TYA8x/right_input0.fastqsanger.gz
-preparing to extract selected reads from: /local/tmp.nAn32TYA8x/left_input0.fastqsanger.gz … done prepping, now search and capture.
-capturing normalized reads from: /local/tmp.nAn32TYA8x/left_input0.fastqsanger.gz
CMD: touch /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: touch /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: ln -sf /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq left.norm.fq
CMD finished (1 seconds)
CMD: ln -sf /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq right.norm.fq
CMD finished (0 seconds)
-removing tmp dir /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads

Normalization complete. See outputs:
/local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq
/local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.gz.normalized_K25_maxC200_minC2_maxCV10000.fq
Tuesday, February 1, 2022: 15:25:18 CMD: touch /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/normalization.ok
Converting input files. (in parallel)Tuesday, February 1, 2022: 15:25:18 CMD: cat /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
Tuesday, February 1, 2022: 15:25:18 CMD: cat /local/tmp.nAn32TYA8x/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
Tuesday, February 1, 2022: 15:26:22 CMD: touch right.fa.ok
Tuesday, February 1, 2022: 15:26:22 CMD: touch left.fa.ok
Tuesday, February 1, 2022: 15:26:22 CMD: touch left.fa.ok right.fa.ok
Tuesday, February 1, 2022: 15:26:22 CMD: cat left.fa right.fa > /local/tmp.nAn32TYA8x/trinity_out_dir/both.fa
Tuesday, February 1, 2022: 15:26:30 CMD: touch /local/tmp.nAn32TYA8x/trinity_out_dir/both.fa.ok

----------- Jellyfish --------------------
– (building a k-mer (25) catalog from reads) –

Running CMD: jellyfish count -t 64 -m 25 -s 34443147819 -o mer_counts.25.asm.jf --canonical /local/tmp.nAn32TYA8x/trinity_out_dir/both.fa

Running CMD: jellyfish dump -L 2 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa

Running CMD: jellyfish histo -t 64 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf

--------------- Inchworm (K=25, asm) ---------------------
– (Linear contig construction from k-mers) –

Running CMD: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/mulled-v1-8bfd939b6449b852af28c673a66720972cbc5543a7cc8d50ff9c6e1f04709fb3/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM -L 25 --no_prune_error_kmers > /local/tmp.nAn32TYA8x/trinity_out_dir/inchworm.DS.fa.tmp
Kmer length set to: 25
Min assembly length set to: 25
Monitor turned on, set to: 1
double stranded mode set
setting number of threads to: 6
-setting parallel iworm mode.
-reading Kmer occurrences…

[0M] Kmers parsed.
…
[163M] Kmers parsed.

read support: 2

Node: 10013 has 6 pairpaths stored:
PairPath [_paths=[[10013, 10053, 10009, 10060, 10004], ]] has read support: 12
PairPath [_paths=[[10013, 10053, 10009, 10060, 10004, 10064, 10018], ]] has read support: 6
PairPath [_paths=[[10013], ]] has read support: 2
PairPath [_paths=[[10013, 10053, 10009, 10060, 10004, 10064, 10018, 9988, 10033], ]] has read support: 2
PairPath [_paths=[[10013, 10053, 10009, 10060], ]] has read support: 2
PairPath [_paths=[[10013, 10053, 10009, 10060], [10018, 9988, 10033]]] has read support: 2

Node: 9950 has 2 pairpaths stored:
PairPath [_paths=[[9950], ]] has read support: 16
PairPath [_paths=[[9950, 9951, 10016, 10002, 9997, 10019], ]] has read support: 6

Node: 10016 has 4 pairpaths stored:
PairPath [_paths=[[10016, 10002, 9997, 10019], ]] has read support: 34
PairPath [_paths=[[10016], ]] has read support: 16
PairPath [_paths=[[10016, 10002, 9997, 10019, 9980, 9972], ]] has read support: 8
PairPath [_paths=[[10016, 10002, 9997, 10019, 9980, 9972, 10021, 9960, 10063, 9962, 9963, 9964], ]] has read support: 2

Node: 10017 has 6 pairpaths stored:
PairPath [_paths=[[10017], ]] has read support: 168
PairPath [_paths=[[10017, 9917, 9918, 9919, 9920, 10063, 9922], ]] has read support: 34
PairPath [_paths=[[10017, 9917, 9918], ]] has read support: 24
PairPath [_paths=[[10017, 9917, 9918, 9919, 9920], ]] has read support: 18
PairPath [_paths=[[10017, 9917, 9918, 9919, 9920, 10063, 9922, 9923], ]] has read support: 16
PairPath [_paths=[[10017, 9917, 9918, 9919], ]] has read support: 8

Node: 10018 has 16 pairpaths stored:
PairPath [_paths=[[10018], ]] has read support: 78
PairPath [_paths=[[10018, 9988, 10033], ]] has read support: 60
PairPath [_paths=[[10018, 9988, 10033, 10032, 10034], ]] has read support: 28
PairPath [_paths=[[10018, 9988, 10033, 10020, 10034], ]] has read support: 18
PairPath [_paths=[[10018, 9988, 10033, 10032], ]] has read support: 8
PairPath [_paths=[[10018, 9988, 10033, 10020, 10034, 10035, 10036], ]] has read support: 6
PairPath [_paths=[[10018, 9988, 10033, 10032, 10034, 10035, 10036, 10037, 10038], ]] has read support: 4
PairPath [_paths=[[10018, 9988, 10033, 10020], ]] has read support: 4
PairPath [_paths=[[10018], [10034, 10035, 10036, 10037]]] has read support: 4
PairPath [_paths=[[10018, 9988, 10033], [10034, 10035, 10036]]] has read support: 2
PairPath [_paths=[[10018, 9988], ]] has read support: 2
PairPath [_paths=[[10018], [10034, 10035, 10036]]] has read support: 2
PairPath [_paths=[[10018, 9988, 10033, 10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9838], ]] has read support: 2
PairPath [_paths=[[10018, 9988, 10033, 10032, 10034, 10035, 10036], ]] has read support: 2
PairPath [_paths=[[10018], [10034, 10035, 10036, 10037, 10038, 10039, 10040]]] has read support: 2
PairPath [_paths=[[10018, 9988, 10033, 10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 2

Node: 10019 has 5 pairpaths stored:
PairPath [_paths=[[10019, 9980, 9972, 10021, 9960, 10063, 9962, 9963, 9964], ]] has read support: 60
PairPath [_paths=[[10019], ]] has read support: 16
PairPath [_paths=[[10019, 9980, 9972], ]] has read support: 4
PairPath [_paths=[[10019, 9980, 9972, 10021, 9960], ]] has read support: 4
PairPath [_paths=[[10019, 9980, 9972, 10021], ]] has read support: 2

Node: 10020 has 8 pairpaths stored:
PairPath [_paths=[[10020], ]] has read support: 8
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 6
PairPath [_paths=[[10020, 10034, 10035, 10036], ]] has read support: 4
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037], ]] has read support: 4
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040], ]] has read support: 2
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037, 10038], ]] has read support: 2
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9838], ]] has read support: 2
PairPath [_paths=[[10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9905], ]] has read support: 2

Node: 10021 has 1 pairpaths stored:
PairPath [_paths=[[10021, 9960, 10063, 9962, 9963, 9964], ]] has read support: 4

Node: 10024 has 5 pairpaths stored:
PairPath [_paths=[[10024], ]] has read support: 144
PairPath [_paths=[[10024, 10060, 9967, 10064, 10017], ]] has read support: 62
PairPath [_paths=[[10024, 10060], ]] has read support: 6
PairPath [_paths=[[10024, 10060, 9967], ]] has read support: 6
PairPath [_paths=[[10024], [10017]]] has read support: 2

Node: 10025 has 6 pairpaths stored:
PairPath [_paths=[[10025], ]] has read support: 58
PairPath [_paths=[[10025, 10016, 10002, 9997, 10019], ]] has read support: 42
PairPath [_paths=[[10025, 10016], ]] has read support: 30
PairPath [_paths=[[10025, 10016, 10002, 9997, 10019, 9980, 9972, 10021], ]] has read support: 4
PairPath [_paths=[[10025, 10016, 10002, 9997, 10019, 9980, 9972, 10021, 9960], ]] has read support: 2
PairPath [_paths=[[10025, 10016, 10002, 9997, 10019, 9980], ]] has read support: 2

Node: 10028 has 4 pairpaths stored:
PairPath [_paths=[[10028], ]] has read support: 56
PairPath [_paths=[[10028, 9827, 10024], ]] has read support: 14
PairPath [_paths=[[10028], [10024]]] has read support: 6
PairPath [_paths=[[10028, 9859, 10024], ]] has read support: 4

Node: 9964 has 1 pairpaths stored:
PairPath [_paths=[[9964], ]] has read support: 16

Node: 10029 has 1 pairpaths stored:
PairPath [_paths=[[10029], ]] has read support: 14

Node: 9838 has 2 pairpaths stored:
PairPath [_paths=[[9838], ]] has read support: 8
PairPath [_paths=[[9838, 10029], ]] has read support: 2

Node: 9967 has 2 pairpaths stored:
PairPath [_paths=[[9967, 10064, 10017], ]] has read support: 44
PairPath [_paths=[[9967], ]] has read support: 8

Node: 10032 has 7 pairpaths stored:
PairPath [_paths=[[10032], ]] has read support: 8
PairPath [_paths=[[10032, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 4
PairPath [_paths=[[10032, 10034, 10035, 10036], ]] has read support: 4
PairPath [_paths=[[10032, 10034, 10035, 10036, 10037], ]] has read support: 4
PairPath [_paths=[[10032, 10034], ]] has read support: 2
PairPath [_paths=[[10032, 10034, 10035, 10036, 10037, 10038, 10039, 10040], ]] has read support: 2
PairPath [_paths=[[10032, 10034, 10035, 10036, 10037, 10038], ]] has read support: 2

Node: 10033 has 5 pairpaths stored:
PairPath [_paths=[[10033, 10032, 10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 8
PairPath [_paths=[[10033, 10020, 10034, 10035, 10036, 10037, 10038, 10039, 10040], ]] has read support: 4
PairPath [_paths=[[10033], ]] has read support: 2
PairPath [_paths=[[10033, 10032, 10034], ]] has read support: 2
PairPath [_paths=[[10033, 10020, 10034, 10035, 10036, 10037], ]] has read support: 2

Node: 9905 has 1 pairpaths stored:
PairPath [_paths=[[9905, 10029], ]] has read support: 6

Node: 10034 has 9 pairpaths stored:
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 36
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9905], ]] has read support: 14
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9905, 10029], ]] has read support: 12
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040], ]] has read support: 12
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9838], ]] has read support: 10
PairPath [_paths=[[10034], ]] has read support: 8
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041], ]] has read support: 4
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], [10029]]] has read support: 2
PairPath [_paths=[[10034, 10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042, 9838, 10029], ]] has read support: 2

Node: 10035 has 1 pairpaths stored:
PairPath [_paths=[[10035, 10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 2

Node: 10036 has 4 pairpaths stored:
PairPath [_paths=[[10036, 10037, 10038, 10039, 10040, 10041, 10042], ]] has read support: 10
PairPath [_paths=[[10036, 10037, 10038, 10039, 10040, 10041, 10042, 9905], ]] has read support: 6
PairPath [_paths=[[10036, 10037, 10038, 10039, 10040, 10041, 10042, 9905, 10029], ]] has read support: 6
PairPath [_paths=[[10036, 10037, 10038, 10039, 10040, 10041, 10042, 9838], ]] has read support: 6

Node: 10037 has 1 pairpaths stored:
PairPath [_paths=[[10037, 10038, 10039, 10040, 10041, 10042, 9838, 10029], ]] has read support: 2

Node: 10039 has 1 pairpaths stored:
PairPath [_paths=[[10039, 10040, 10041, 10042, 9905, 10029], ]] has read support: 6

Node: 10040 has 5 pairpaths stored:
PairPath [_paths=[[10040, 10041, 10042, 9838], ]] has read support: 12
PairPath [_paths=[[10040], ]] has read support: 6
PairPath [_paths=[[10040, 10041, 10042, 9905], ]] has read support: 4
PairPath [_paths=[[10040, 10041, 10042], ]] has read support: 4
PairPath [_paths=[[10040, 10041, 10042, 9905, 10029], ]] has read support: 2

Node: 10042 has 4 pairpaths stored:
PairPath [_paths=[[10042, 9838], ]] has read support: 14
PairPath [_paths=[[10042, 9905, 10029], ]] has read support: 8
PairPath [_paths=[[10042], ]] has read support: 4
PairPath [_paths=[[10042, 9838, 10029], ]] has read support: 4

Node: 9980 has 1 pairpaths stored:
PairPath [_paths=[[9980, 9972, 10021, 9960, 10063, 9962, 9963, 9964], ]] has read support: 2

Node: 10045 has 4 pairpaths stored:
PairPath [_paths=[[10045, 10046, 9985, 10053, 10025], ]] has read support: 28
PairPath [_paths=[[10045], ]] has read support: 8
PairPath [_paths=[[10045, 10046, 9985, 10053], ]] has read support: 4
PairPath [_paths=[[10045, 10046, 10013, 10053, 10009, 10060, 10004, 10064, 10018], ]] has read support: 2

Node: 10046 has 8 pairpaths stored:
PairPath [_paths=[[10046, 10013, 10053, 10009, 10060, 10004, 10064, 10018], ]] has read support: 28
PairPath [_paths=[[10046, 10013, 10053, 10009], [10018]]] has read support: 10
PairPath [_paths=[[10046, 10013, 10053, 10009, 10060, 10004], ]] has read support: 6
PairPath [_paths=[[10046, 10013, 10053, 10009], [10033, 10032, 10034]]] has read support: 2
PairPath [_paths=[[10046, 10013, 10053, 10009, 10060], ]] has read support: 2
PairPath [_paths=[[10046, 9985, 10053, 10025, 10016, 10002, 9997, 10019], ]] has read support: 2
PairPath [_paths=[[10046, 10013, 10053, 10009], ]] has read support: 2
PairPath [_paths=[[10046, 9985, 10053, 10025], ]] has read support: 2

Node: 9918 has 2 pairpaths stored:
PairPath [_paths=[[9918, 9919, 9920, 10063, 9922, 9923], ]] has read support: 20
PairPath [_paths=[[9918, 9919, 9920, 10063, 9922], ]] has read support: 16

Total number of pairpaths: 151

***** PairPath Counts *****
Node: 2032 has 8 pairpaths stored:
PairPath [_paths=[[2032, 2033, 2034], ]] has read support: 16
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051], ]] has read support: 12
PairPath [_paths=[[2032], ]] has read support: 12
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048], ]] has read support: 6
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 4
PairPath [_paths=[[2032, 2033], ]] has read support: 2
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046], ]] has read support: 2
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046, 2045], ]] has read support: 2

Node: 2048 has 1 pairpaths stored:
PairPath [_paths=[[2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 2

Node: 2033 has 3 pairpaths stored:
PairPath [_paths=[[2033, 2034, 2053, 2051, 2048, 2047], ]] has read support: 2
PairPath [_paths=[[2033, 2034, 2053, 2051], ]] has read support: 2
PairPath [_paths=[[2033, 2034, 2053, 2051, 2048], ]] has read support: 2

Node: 2034 has 7 pairpaths stored:
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047], ]] has read support: 12
PairPath [_paths=[[2034], ]] has read support: 8
PairPath [_paths=[[2034, 2053, 2051], ]] has read support: 6
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 4
PairPath [_paths=[[2034, 2053, 2051, 2048], ]] has read support: 4
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046], ]] has read support: 2
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 2

Node: 2019 has 1 pairpaths stored:
PairPath [_paths=[[2019, 2053, 2051], ]] has read support: 2

Node: 2051 has 5 pairpaths stored:
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 20
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 12
PairPath [_paths=[[2051], ]] has read support: 10
PairPath [_paths=[[2051, 2048, 2047], ]] has read support: 2
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045], ]] has read support: 2

Node: 2053 has 1 pairpaths stored:
PairPath [_paths=[[2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 4

Node: 2045 has 2 pairpaths stored:
PairPath [_paths=[[2045, 2043, 2052, 2030, 2031], ]] has read support: 12
PairPath [_paths=[[2045], ]] has read support: 8

Node: 2030 has 1 pairpaths stored:
PairPath [_paths=[[2030, 2031], ]] has read support: 2

Node: 2046 has 1 pairpaths stored:
PairPath [_paths=[[2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 6

Node: 2031 has 1 pairpaths stored:
PairPath [_paths=[[2031], ]] has read support: 78

Total number of pairpaths: 31

***** PairPath Counts *****
Node: 2032 has 8 pairpaths stored:
PairPath [_paths=[[2032, 2033, 2034], ]] has read support: 16
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051], ]] has read support: 12
PairPath [_paths=[[2032], ]] has read support: 12
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048], ]] has read support: 6
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 4
PairPath [_paths=[[2032, 2033], ]] has read support: 2
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046], ]] has read support: 2
PairPath [_paths=[[2032, 2033, 2034, 2053, 2051, 2048, 2047, 2046, 2045], ]] has read support: 2

Node: 2048 has 1 pairpaths stored:
PairPath [_paths=[[2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 2

Node: 2033 has 3 pairpaths stored:
PairPath [_paths=[[2033, 2034, 2053, 2051, 2048, 2047], ]] has read support: 2
PairPath [_paths=[[2033, 2034, 2053, 2051], ]] has read support: 2
PairPath [_paths=[[2033, 2034, 2053, 2051, 2048], ]] has read support: 2

Node: 2034 has 7 pairpaths stored:
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047], ]] has read support: 12
PairPath [_paths=[[2034], ]] has read support: 8
PairPath [_paths=[[2034, 2053, 2051], ]] has read support: 6
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 4
PairPath [_paths=[[2034, 2053, 2051, 2048], ]] has read support: 4
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046], ]] has read support: 2
PairPath [_paths=[[2034, 2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 2

Node: 2019 has 1 pairpaths stored:
PairPath [_paths=[[2019, 2053, 2051], ]] has read support: 2

Node: 2051 has 5 pairpaths stored:
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 20
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045, 2043, 2052], ]] has read support: 12
PairPath [_paths=[[2051], ]] has read support: 10
PairPath [_paths=[[2051, 2048, 2047], ]] has read support: 2
PairPath [_paths=[[2051, 2048, 2047, 2046, 2045], ]] has read support: 2

Node: 2053 has 1 pairpaths stored:
PairPath [_paths=[[2053, 2051, 2048, 2047, 2046, 2045, 2043, 2052, 2030, 2031], ]] has read support: 4

Node: 2045 has 2 pairpaths stored:
Pair

The standard error output is empty,

Tool Exit Code:	2
Job Messages	* { “code_desc”: “”, “desc”: “Fatal error: Exit code 2 ()”, “error_level”: 3, “exit_code”: 2, “type”: “exit_code” }

Any idea what is happening?

gallardoalba · February 3, 2022, 10:48am

Hi @Asrix,
could you share your history with me? I’ll have a look at it.

Regards

Asrix · February 3, 2022, 5:49pm

https://usegalaxy.org/u/asr/h/unnamed-history

gallardoalba · February 9, 2022, 3:06pm

Hi @Asrix,
I have checked the history, but unfortunately, it doesn’t contain meaningful information about the cause of the error.

Asrix · February 9, 2022, 5:16pm

Okay. It is the second time it has done that. I removed everything after the first time and tried again, so it is a reoccurring problem. It might be that the error is misleading and it is actually some other problem, but hard to tell.

luweidong · June 11, 2023, 12:34pm

Hi, Anna Rix,

I met the similar problem as you, have you resolved that?

jennaj · June 12, 2023, 8:21pm

@luweidong Please continue in the same original topic. An error occurred when I used Trinity to analysis my RNA-seq data (clean paired-end fq.gz files) - #22 by luweidong

Topic		Replies	Views
Trinity - assembly error -- Input problems usegalaxy.org support	1	807	June 29, 2020
Trinity tool error usegalaxy.eu support transcriptomics	3	493	August 29, 2022
Error with Trinity De Novo Assembly in GVL 4.4.0 install usegalaxy.org support gvl , conda-dependency	5	1527	February 20, 2019
Trinity error in usegalaxy.org site usegalaxy.org support	6	1293	April 15, 2019
Error with de novo assembly using Trintiy usegalaxy.org support assembly , transcriptomics , server-open-issue , rna-seq	4	290	August 18, 2023

Trinity Assembly

-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------

------------ In silico Read Normalization ---------------------
– (Removing Excess Reads Beyond 200 Coverage –

running normalization on reads: $VAR1 = [

----------- Jellyfish --------------------
– (building a k-mer catalog from reads) –

----------- Jellyfish --------------------
– (building a k-mer (25) catalog from reads) –

--------------- Inchworm (K=25, asm) ---------------------
– (Linear contig construction from k-mers) –

Total number of pairpaths: 151

Total number of pairpaths: 31

Trinity Assembly

-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------

------------ In silico Read Normalization --------------------- – (Removing Excess Reads Beyond 200 Coverage –

running normalization on reads: $VAR1 = [

----------- Jellyfish -------------------- – (building a k-mer catalog from reads) –

----------- Jellyfish -------------------- – (building a k-mer (25) catalog from reads) –

--------------- Inchworm (K=25, asm) --------------------- – (Linear contig construction from k-mers) –

Total number of pairpaths: 151

Total number of pairpaths: 31

Related Topics

------------ In silico Read Normalization ---------------------
– (Removing Excess Reads Beyond 200 Coverage –

----------- Jellyfish --------------------
– (building a k-mer catalog from reads) –

----------- Jellyfish --------------------
– (building a k-mer (25) catalog from reads) –

--------------- Inchworm (K=25, asm) ---------------------
– (Linear contig construction from k-mers) –