[2024-01-24 12:13:28,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference
[2024-01-24 12:13:30,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,395] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,395] [INFO] Running command: gunzip -c /var/lib/cwl/stga92bc705-7aad-4ca6-b5f7-39037dd75638/GCF_002104735.1_ASM210473v1_genomic.fna.gz | prodigal -d GCF_002104735.1_ASM210473v1_genomic.fna/cds.fna -a GCF_002104735.1_ASM210473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:48,744] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:48,744] [INFO] Task started: HMMsearch
[2024-01-24 12:13:48,744] [INFO] Running command: hmmsearch --tblout GCF_002104735.1_ASM210473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/reference_markers.hmm GCF_002104735.1_ASM210473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:49,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:49,123] [INFO] Found 6/6 markers.
[2024-01-24 12:13:49,169] [INFO] Query marker FASTA was written to GCF_002104735.1_ASM210473v1_genomic.fna/markers.fasta
[2024-01-24 12:13:49,169] [INFO] Task started: Blastn
[2024-01-24 12:13:49,169] [INFO] Running command: blastn -query GCF_002104735.1_ASM210473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/reference_markers.fasta -out GCF_002104735.1_ASM210473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:50,403] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:50,408] [INFO] Selected 9 target genomes.
[2024-01-24 12:13:50,408] [INFO] Target genome list was writen to GCF_002104735.1_ASM210473v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:50,412] [INFO] Task started: fastANI
[2024-01-24 12:13:50,412] [INFO] Running command: fastANI --query /var/lib/cwl/stga92bc705-7aad-4ca6-b5f7-39037dd75638/GCF_002104735.1_ASM210473v1_genomic.fna.gz --refList GCF_002104735.1_ASM210473v1_genomic.fna/target_genomes.txt --output GCF_002104735.1_ASM210473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:05,819] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:05,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:05,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:05,830] [INFO] Found 9 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 12:14:05,830] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:14:05,831] [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
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	100.0	1770	1778	95	inconclusive
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	99.9978	1776	1778	95	inconclusive
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	99.9975	1778	1778	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	98.658	1661	1778	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	98.653	1659	1778	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	98.4368	1473	1778	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	97.7085	1598	1778	95	inconclusive
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	92.5258	1529	1778	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	92.5234	1571	1778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:05,834] [INFO] DFAST Taxonomy check result was written to GCF_002104735.1_ASM210473v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:05,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:05,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:05,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/checkm_data
[2024-01-24 12:14:05,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:05,911] [INFO] Task started: CheckM
[2024-01-24 12:14:05,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104735.1_ASM210473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104735.1_ASM210473v1_genomic.fna/checkm_input GCF_002104735.1_ASM210473v1_genomic.fna/checkm_result
[2024-01-24 12:14:58,523] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:58,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:58,550] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:58,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:58,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104735.1_ASM210473v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:58,551] [INFO] Task started: Blastn
[2024-01-24 12:14:58,551] [INFO] Running command: blastn -query GCF_002104735.1_ASM210473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a08c648-3db8-4f3b-9342-c284a0a38ec8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104735.1_ASM210473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,420] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,424] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:00,425] [INFO] Target genome list was writen to GCF_002104735.1_ASM210473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:00,437] [INFO] Task started: fastANI
[2024-01-24 12:15:00,437] [INFO] Running command: fastANI --query /var/lib/cwl/stga92bc705-7aad-4ca6-b5f7-39037dd75638/GCF_002104735.1_ASM210473v1_genomic.fna.gz --refList GCF_002104735.1_ASM210473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104735.1_ASM210473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:26,180] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:26,194] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:26,195] [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_000277125.1	s__Mycobacterium intracellulare	98.6288	1663	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	conclusive
GCF_010731675.1	s__Mycobacterium marseillense	92.5234	1571	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_001667315.1	s__Mycobacterium sp001667315	90.8819	1476	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	90.0579	1400	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741445.1	s__Mycobacterium avium	87.7332	1428	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_001953985.1	s__Mycobacterium colombiense_B	87.3776	1463	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_010731775.1	s__Mycobacterium mantenii	86.9413	1486	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_001665875.1	s__Mycobacterium sp001665875	86.9398	1381	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667145.1	s__Mycobacterium sp001667145	86.2688	1348	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	84.5735	1264	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	84.3968	1295	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_900240975.1	s__Mycobacterium sp900240975	84.2009	1272	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_010730745.1	s__Mycobacterium heidelbergense	84.1823	1161	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667735.1	s__Mycobacterium sp001667735	84.1383	1263	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001907675.1	s__Mycobacterium paraffinicum	84.1374	1332	1778	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	84.014	1282	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_010730195.1	s__Mycobacterium conspicuum	82.3747	1183	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,197] [INFO] GTDB search result was written to GCF_002104735.1_ASM210473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:26,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:26,201] [INFO] DFAST_QC result json was written to GCF_002104735.1_ASM210473v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:26,202] [INFO] DFAST_QC completed!
[2024-01-24 12:15:26,202] [INFO] Total running time: 0h1m57s