I am working with a modified ARTIC workflow with additional fastp filtering steps described by Maio et al. on May 15th. The BWA-MEM step on the workflow has been giving more errors than normal, but I figured site resources were being worked on or something else was going on. I went to execute the modified workflow and got the following message:
The server could not complete the request. Please contact the Galaxy Team if this error persists.
{“new_history_name”: “C19_005 - COVID Assembly (DP=400X,AF=0.03, 0.0001 SB Filter, MASK, fastp Filters) Beta 2.0”,
“history_id”: null,
“resource_params”: {},
“replacement_params”: {},
“parameters”: {
“0”: {
“input”: {
“values”: [
{
“hid”: 50,
“id”: “bbd44e69cb8906b5d96d02efe29cb2ac”,
“keep”: false,
“name”: “ARTIC_SARS_CoV-2_amplicon_info_v3_Prime.tsv”,
“src”: “hda”,
“tags”: []
}
],
“batch”: false
}
},
“1”: {
“input”: {
“values”: [
{
“hid”: 52,
“id”: “bbd44e69cb8906b5ee20e41c8d815ee8”,
“keep”: false,
“name”: “nCoV-2019_v3.bed (as bed)”,
“src”: “hda”,
“tags”: []
}
],
“batch”: false
}
},
“2”: {
“input”: {
“values”: [
{
“hid”: 49,
“id”: “bbd44e69cb8906b54fce2385a595d8a4”,
“keep”: false,
“name”: “MN_908947.fasta”,
“src”: “hda”,
“tags”: []
}
],
“batch”: false
}
},
“3”: {
“input”: {
“values”: [
{
“id”: “ae18630e474d2f95”,
“src”: “hdca”,
“hid”: 79,
“name”: “C19_005”,
“keep”: true,
“tags”: []
}
],
“batch”: false
}
},
“5”: {
“single_paired|single_paired_selector”: “paired”,
“single_paired|adapter_trimming_options|disable_adapter_trimming”: “false”,
“single_paired|adapter_trimming_options|adapter_sequence1”: “”,
“single_paired|adapter_trimming_options|adapter_sequence2”: “”,
“single_paired|global_trimming_options|trim_front1”: “15”,
“single_paired|global_trimming_options|trim_tail1”: “15”,
“single_paired|global_trimming_options|trim_front2”: “15”,
“single_paired|global_trimming_options|trim_tail2”: “15”,
“overrepresented_sequence_analysis|overrepresentation_analysis”: “false”,
“overrepresented_sequence_analysis|overrepresentation_sampling”: “”,
“filter_options|quality_filtering_options|disable_quality_filtering”: “false”,
“filter_options|quality_filtering_options|qualified_quality_phred”: “35”,
“filter_options|quality_filtering_options|unqualified_percent_limit”: “”,
“filter_options|quality_filtering_options|n_base_limit”: “”,
“filter_options|length_filtering_options|disable_length_filtering”: “false”,
“filter_options|length_filtering_options|length_required”: “”,
“filter_options|low_complexity_filter|enable_low_complexity_filter”: “false”,
“filter_options|low_complexity_filter|complexity_threshold”: “”,
“read_mod_options|polyg_tail_trimming|trimming_select”: “”,
“read_mod_options|polyg_tail_trimming|poly_g_min_len”: “”,
“read_mod_options|polyx_tail_trimming|polyx_trimming_select”: “-x”,
“read_mod_options|polyx_tail_trimming|poly_x_min_len”: “”,
“read_mod_options|umi_processing|umi”: “false”,
“read_mod_options|umi_processing|umi_loc”: “”,
“read_mod_options|umi_processing|umi_len”: “”,
“read_mod_options|umi_processing|umi_prefix”: “”,
“read_mod_options|cutting_by_quality_options|cut_by_quality5”: “false”,
“read_mod_options|cutting_by_quality_options|cut_by_quality3”: “true”,
“read_mod_options|cutting_by_quality_options|cut_window_size”: “”,
“read_mod_options|cutting_by_quality_options|cut_mean_quality”: “30”,
“read_mod_options|base_correction_options|correction”: “false”,
“output_options|report_html”: “true”,
“output_options|report_json”: “true”,
“__job_resource|__job_resource__select”: “no”
},
“6”: {
“reference_source|reference_source_selector”: “history”,
“reference_source|index_a”: “auto”,
“fastq_input|fastq_input_selector”: “paired”,
“fastq_input|iset_stats”: “”,
“rg|rg_selector”: “do_not_set”,
“analysis_type|analysis_type_selector”: “illumina”,
“__job_resource|__job_resource__select”: “no”
},
“8”: {
“mode|outtype”: “selected_reads”,
“mode|filter_config|cond_region|select_region”: “no”,
“mode|filter_config|cond_rg|select_rg”: “no”,
“mode|filter_config|quality”: “20”,
“mode|filter_config|library”: “”,
“mode|filter_config|cigarcons”: “”,
“mode|filter_config|inclusive_filter”: [
“1”
],
“mode|filter_config|exclusive_filter”: [
“4”,
“8”,
“256”
],
“mode|filter_config|exclusive_filter_all”: null,
“mode|subsample_config|subsampling_mode|select_subsample”: “fraction”,
“mode|subsample_config|subsampling_mode|factor”: “1.0”,
“mode|subsample_config|subsampling_mode|seed”: “”,
“mode|output_options|reads_report_type”: “retained”,
“mode|output_options|complementary_output”: “false”,
“mode|output_options|adv_output|collapsecigar”: “false”,
“mode|output_options|output_format|oformat”: “bam”,
“mode|output_options|output_format|fmtopt”: “-b”,
“addref_cond|addref_select”: “no”
},
“9”: {
“input_type|input_type_select”: “bam”,
“report|report_select”: “bg”,
“report|zero_regions”: “false”,
“report|scale”: “1.0”,
“split”: “false”,
“strand”: “”,
“d”: “false”,
“dz”: “false”,
“five”: “false”,
“three”: “false”
},
“10”: {
“coverage_cond|coverage_select”: “no”,
“remove_dups”: “false”,
“split_output_cond|split_output_selector”: “no”,
“filter_by_flags|filter_flags”: “nofilter”,
“gc_depth”: “”,
“insert_size”: “”,
“read_length”: “”,
“most_inserts”: “”,
“trim_quality”: “”,
“addref_cond|addref_select”: “no”,
“cond_region|select_region”: “no”,
“sparse”: “false”,
“remove_overlaps”: “false”,
“cov_threshold”: “”
},
“11”: {
“primer|source”: “history”,
“min_len”: “1”,
“min_qual”: “0”,
“window_width”: “4”,
“inc_primers”: “true”
},
“12”: {
“code”: “4<400"
},
"13": {
"reference_source|ref_selector": "history",
"adv_options|keepflags": "false",
"adv_options|bq2_handling|replace_bq2": "keep",
"adv_options|bq2_handling|defqual": "2",
"__job_resource|__job_resource__select": "no"
},
"14": {
"strategy|selector": "dindel",
"strategy|reference_source|ref_selector": "history"
},
"15": {
"stats_regions|region_select": "all",
"per_base_coverage": "false",
"duplicate_skipping": "0",
"plot_specific|n_bins": "400",
"plot_specific|paint_chromosome_limits": "true",
"plot_specific|genome_gc_distr": null,
"plot_specific|homopolymer_size": "3",
"__job_resource|__job_resource__select": "no"
},
"16": {
"reference_source|ref_selector": "history",
"regions|restrict_to_region": "genome",
"variant_types": "--call-indels",
"call_control|set_call_options": "yes",
"call_control|coverage|min_cov": "5",
"call_control|coverage|max_depth": "1000000",
"call_control|pe|use_orphan": "false",
"call_control|bc_quals|min_bq": "30",
"call_control|bc_quals|min_alt_bq": "30",
"call_control|bc_quals|alt_bq|modify": "",
"call_control|align_quals|alnqual|use_alnqual": "",
"call_control|align_quals|alnqual|alnqual_choice|alnquals_to_use": "",
"call_control|align_quals|alnqual|alnqual_choice|extended_baq": "true",
"call_control|map_quals|min_mq": "20",
"call_control|map_quals|use_mq|no_mq": "",
"call_control|map_quals|use_mq|max_mq": "255",
"call_control|source_qual|use_src_qual|src_qual": "",
"call_control|joint_qual|min_jq": "0",
"call_control|joint_qual|min_alt_jq": "0",
"call_control|joint_qual|def_alt_jq": "0",
"filter_control|filter_type": "set_custom",
"filter_control|sig": "0.0005",
"filter_control|bonf": "0",
"filter_control|others": "false",
"__job_resource|__job_resource__select": "no"
},
"17": {
"join_identifier": "_"
},
"18": {
"filter_by_type|keep_only": "",
"filter_by_type|qual|snvqual_filter|snvqual": "no",
"filter_by_type|qual|indelqual_filter|indelqual": "no",
"coverage|cov_min": "5",
"coverage|cov_max": "0",
"af|af_min": "0.05",
"af|af_max": "0.95",
"sb|sb_filter|strand_bias": "no",
"flag_or_drop": ""
},
"19": {
"results_0|software_cond|software": "fastp",
"results_1|software_cond|software": "samtools",
"results_1|software_cond|output_0|type|type": "stats",
"results_2|software_cond|software": "qualimap",
"title": "",
"comment": "",
"flat": "false",
"saveLog": "false"
},
"21": {
"reference_source|ref_selector": "history",
"regions|restrict_to_region": "genome",
"variant_types": "--call-indels",
"call_control|set_call_options": "yes",
"call_control|coverage|min_cov": "5",
"call_control|coverage|max_depth": "1000000",
"call_control|pe|use_orphan": "false",
"call_control|bc_quals|min_bq": "30",
"call_control|bc_quals|min_alt_bq": "30",
"call_control|bc_quals|alt_bq|modify": "",
"call_control|align_quals|alnqual|use_alnqual": "",
"call_control|align_quals|alnqual|alnqual_choice|alnquals_to_use": "",
"call_control|align_quals|alnqual|alnqual_choice|extended_baq": "true",
"call_control|map_quals|min_mq": "20",
"call_control|map_quals|use_mq|no_mq": "",
"call_control|map_quals|use_mq|max_mq": "255",
"call_control|source_qual|use_src_qual|src_qual": "",
"call_control|joint_qual|min_jq": "0",
"call_control|joint_qual|min_alt_jq": "0",
"call_control|joint_qual|def_alt_jq": "0",
"filter_control|filter_type": "set_custom",
"filter_control|sig": "0.0005",
"filter_control|bonf": "0",
"filter_control|others": "false",
"__job_resource|__job_resource__select": "no"
},
"22": {
"reference_source|reference_source_selector": "history",
"isect_union": "-i",
"invert": "true",
"window_size": "0",
"loci": "false",
"adv_options|adv_options_selector": "no"
},
"23": {
"replacements_0|find_pattern": "^(#CHROM.+)”,
“replacements_0|replace_pattern”: “##FILTER=<ID=AmpliconRemoval,Description=“Variant removed upon removal of amplicon”>\n\1”,
“replacements_1|find_pattern”: “(.+\t)PASS(\t.+)”,
“replacements_1|replace_pattern”: “\1AmpliconRemoval\2”
},
“24”: {
“reference_source|reference_source_selector”: “history”,
“isect_union”: “-u”,
“invert”: “false”,
“window_size”: “0”,
“loci”: “false”,
“adv_options|adv_options_selector”: “no”
},
“25”: {
“filter_by_type|keep_only”: “”,
“filter_by_type|qual|snvqual_filter|snvqual”: “no”,
“filter_by_type|qual|indelqual_filter|indelqual”: “no”,
“coverage|cov_min”: “400”,
“coverage|cov_max”: “0”,
“af|af_min”: “0.05”,
“af|af_max”: “0.0”,
“sb|sb_filter|strand_bias”: “mtc”,
“sb|sb_filter|sb_alpha”: “0.001”,
“sb|sb_filter|sb_mtc”: “fdr”,
“sb|sb_filter|sb_compound”: “true”,
“sb|sb_filter|sb_indels”: “false”,
“flag_or_drop”: “–print-all”
},
“26”: {
“inputFormat”: “vcf”,
“genome_version”: “NC_045512.2”,
“outputConditional|outputFormat”: “vcf”,
“csvStats”: “false”,
“udLength”: “0”,
“annotations”: [
“-formatEff”,
“-classic”
],
“intervals”: null,
“transcripts”: null,
“filterOut”: [
“-no-downstream”,
“-no-intergenic”,
“-no-upstream”
],
“filter|specificEffects”: “no”,
“offset”: “default”,
“chr”: “”,
“generate_stats”: “true”,
“noLog”: “true”
},
“27”: {
“filter_repeat_0|filter_type”: “-f”,
“filter_repeat_0|filter_value”: “FILTER = PASS”,
“filter_sites”: “false”,
“tag_pass”: “false”,
“tag_fail”: “false”,
“append_filter”: “false”,
“allele_tag”: “false”,
“invert”: “false”,
“or”: “false”,
“region”: “”
},
“28”: {
“extract”: “CHROM POS REF ALT FILTER DP AF SB DP4 EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[*].CODON”,
“one_effect_per_line”: “false”,
“separator”: “”,
“empty_text”: “”
},
“29”: {
“reference_source|reference_source_selector”: “history”,
“sec_default|iupac_codes”: “false”,
“sec_default|sample”: “”,
“sec_default|select_haplotype”: null,
“chain”: “false”,
“rename”: “true”
}
},
“parameters_normalized”: true,
“batch”: true
}
I have tried to execute the workflow on different samples and still get the same error. I tried one of the earlier builds of the modified workflow that has worked before and the same error message was received. Any help or feedback would be appreciated. Thank you in advance!