[2024-01-24 11:05:28,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,092] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference
[2024-01-24 11:05:29,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,626] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg033145bf-7ff8-43f8-84bf-3ff46be39600/GCF_025823185.1_ASM2582318v1_genomic.fna.gz | prodigal -d GCF_025823185.1_ASM2582318v1_genomic.fna/cds.fna -a GCF_025823185.1_ASM2582318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:50,580] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:50,580] [INFO] Task started: HMMsearch
[2024-01-24 11:05:50,580] [INFO] Running command: hmmsearch --tblout GCF_025823185.1_ASM2582318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/reference_markers.hmm GCF_025823185.1_ASM2582318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:50,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:50,954] [INFO] Found 6/6 markers.
[2024-01-24 11:05:51,009] [INFO] Query marker FASTA was written to GCF_025823185.1_ASM2582318v1_genomic.fna/markers.fasta
[2024-01-24 11:05:51,009] [INFO] Task started: Blastn
[2024-01-24 11:05:51,009] [INFO] Running command: blastn -query GCF_025823185.1_ASM2582318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/reference_markers.fasta -out GCF_025823185.1_ASM2582318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:52,255] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:52,258] [INFO] Selected 28 target genomes.
[2024-01-24 11:05:52,258] [INFO] Target genome list was writen to GCF_025823185.1_ASM2582318v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:52,267] [INFO] Task started: fastANI
[2024-01-24 11:05:52,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg033145bf-7ff8-43f8-84bf-3ff46be39600/GCF_025823185.1_ASM2582318v1_genomic.fna.gz --refList GCF_025823185.1_ASM2582318v1_genomic.fna/target_genomes.txt --output GCF_025823185.1_ASM2582318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:26,347] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:26,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:26,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:26,372] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:26,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:26,373] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.6847	1124	2141	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.6531	1160	2141	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.1545	1017	2141	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.9771	944	2141	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	79.9664	951	2141	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	79.7678	946	2141	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	79.7674	941	2141	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	79.7404	926	2141	95	below_threshold
Mycolicibacterium phocaicum	strain=DSM 45104	GCA_005670655.1	319706	319706	type	True	79.663	810	2141	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	79.661	822	2141	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	79.6559	897	2141	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	79.6371	815	2141	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.6063	809	2141	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.5831	904	2141	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	79.5566	916	2141	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.5184	626	2141	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.507	912	2141	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.4999	907	2141	95	below_threshold
Mycolicibacterium wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	79.4019	909	2141	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	79.3425	851	2141	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.2487	810	2141	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.2253	793	2141	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.9938	812	2141	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	78.6999	669	2141	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	78.6511	683	2141	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	78.6403	673	2141	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	78.5317	638	2141	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	78.4729	651	2141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:26,374] [INFO] DFAST Taxonomy check result was written to GCF_025823185.1_ASM2582318v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:26,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:26,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:26,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/checkm_data
[2024-01-24 11:06:26,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:26,436] [INFO] Task started: CheckM
[2024-01-24 11:06:26,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823185.1_ASM2582318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823185.1_ASM2582318v1_genomic.fna/checkm_input GCF_025823185.1_ASM2582318v1_genomic.fna/checkm_result
[2024-01-24 11:07:37,352] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:37,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:37,378] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:37,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:37,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823185.1_ASM2582318v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:37,379] [INFO] Task started: Blastn
[2024-01-24 11:07:37,379] [INFO] Running command: blastn -query GCF_025823185.1_ASM2582318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc146b38-61ba-4f1f-aa4d-5ccb0385341d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823185.1_ASM2582318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:39,146] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:39,150] [INFO] Selected 14 target genomes.
[2024-01-24 11:07:39,151] [INFO] Target genome list was writen to GCF_025823185.1_ASM2582318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:39,171] [INFO] Task started: fastANI
[2024-01-24 11:07:39,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg033145bf-7ff8-43f8-84bf-3ff46be39600/GCF_025823185.1_ASM2582318v1_genomic.fna.gz --refList GCF_025823185.1_ASM2582318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823185.1_ASM2582318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:59,140] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:59,154] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:07:59,154] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_008329535.1	s__Mycobacterium sp008329535	86.3775	1588	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426545.1	s__Mycobacterium sp001426545	85.2807	1544	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	85.2655	1516	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCA_016462545.1	s__Mycobacterium sp016462545	82.0944	1248	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	82.0766	1249	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439015.1	s__Mycobacterium hodleri_A	81.5517	1168	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731735.1	s__Mycobacterium sediminis	80.9393	1134	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	80.6554	1162	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	79.8715	974	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499995.1	s__Mycobacterium sp001499995	79.7393	909	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	79.5658	869	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_001500065.1	s__Mycobacterium sp001500065	79.2647	777	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	78.8062	687	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666835.1	s__Mycobacterium sp001666835	78.4683	633	2141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:59,156] [INFO] GTDB search result was written to GCF_025823185.1_ASM2582318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:59,156] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:59,164] [INFO] DFAST_QC result json was written to GCF_025823185.1_ASM2582318v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:59,165] [INFO] DFAST_QC completed!
[2024-01-24 11:07:59,165] [INFO] Total running time: 0h2m31s