[2024-01-24 12:14:34,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,064] [INFO] DQC Reference Directory: /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference
[2024-01-24 12:14:35,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,221] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,221] [INFO] Running command: gunzip -c /var/lib/cwl/stgb502e466-7660-48f1-a7d9-1b7aeb4fc529/GCF_010722995.1_ASM1072299v1_genomic.fna.gz | prodigal -d GCF_010722995.1_ASM1072299v1_genomic.fna/cds.fna -a GCF_010722995.1_ASM1072299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:55,006] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:55,006] [INFO] Task started: HMMsearch
[2024-01-24 12:14:55,006] [INFO] Running command: hmmsearch --tblout GCF_010722995.1_ASM1072299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/reference_markers.hmm GCF_010722995.1_ASM1072299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:55,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:55,449] [INFO] Found 6/6 markers.
[2024-01-24 12:14:55,500] [INFO] Query marker FASTA was written to GCF_010722995.1_ASM1072299v1_genomic.fna/markers.fasta
[2024-01-24 12:14:55,501] [INFO] Task started: Blastn
[2024-01-24 12:14:55,501] [INFO] Running command: blastn -query GCF_010722995.1_ASM1072299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/reference_markers.fasta -out GCF_010722995.1_ASM1072299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,724] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,726] [INFO] Selected 24 target genomes.
[2024-01-24 12:14:56,726] [INFO] Target genome list was writen to GCF_010722995.1_ASM1072299v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,733] [INFO] Task started: fastANI
[2024-01-24 12:14:56,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgb502e466-7660-48f1-a7d9-1b7aeb4fc529/GCF_010722995.1_ASM1072299v1_genomic.fna.gz --refList GCF_010722995.1_ASM1072299v1_genomic.fna/target_genomes.txt --output GCF_010722995.1_ASM1072299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:24,463] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:24,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:24,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:24,477] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:24,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:24,478] [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 tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	98.0564	1924	2277	95	conclusive
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	97.9878	1937	2277	95	conclusive
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	81.2825	1160	2277	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.6944	768	2277	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.6356	760	2277	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.4634	944	2277	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.4391	955	2277	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.2457	634	2277	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.223	1001	2277	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.211	993	2277	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.1171	932	2277	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.1149	944	2277	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.9986	851	2277	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.8845	959	2277	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7375	839	2277	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.5755	787	2277	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.5374	841	2277	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.5325	839	2277	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.3344	789	2277	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.2128	805	2277	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	79.1438	711	2277	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	79.0963	712	2277	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	78.7839	641	2277	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	78.761	627	2277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:24,479] [INFO] DFAST Taxonomy check result was written to GCF_010722995.1_ASM1072299v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:24,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:24,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:24,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/checkm_data
[2024-01-24 12:15:24,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:24,540] [INFO] Task started: CheckM
[2024-01-24 12:15:24,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010722995.1_ASM1072299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010722995.1_ASM1072299v1_genomic.fna/checkm_input GCF_010722995.1_ASM1072299v1_genomic.fna/checkm_result
[2024-01-24 12:17:44,466] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:44,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:44,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:44,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:44,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010722995.1_ASM1072299v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:44,482] [INFO] Task started: Blastn
[2024-01-24 12:17:44,482] [INFO] Running command: blastn -query GCF_010722995.1_ASM1072299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7dd5ce1-eb54-4d59-ae38-07272c8464da/dqc_reference/reference_markers_gtdb.fasta -out GCF_010722995.1_ASM1072299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:46,408] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:46,411] [INFO] Selected 21 target genomes.
[2024-01-24 12:17:46,411] [INFO] Target genome list was writen to GCF_010722995.1_ASM1072299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:46,420] [INFO] Task started: fastANI
[2024-01-24 12:17:46,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgb502e466-7660-48f1-a7d9-1b7aeb4fc529/GCF_010722995.1_ASM1072299v1_genomic.fna.gz --refList GCF_010722995.1_ASM1072299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010722995.1_ASM1072299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:11,669] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:11,681] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:11,681] [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_010725885.1	s__Mycobacterium tokaiense	98.0564	1924	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	conclusive
GCF_001984215.1	s__Mycobacterium sp001984215	84.6437	1525	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015710575.1	s__Mycobacterium sp015710575	81.2922	1158	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	-
GCF_010726955.1	s__Mycobacterium fallax	80.6567	772	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_002592005.1	s__Mycobacterium palauense	80.4054	961	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.2589	833	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.2085	993	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002086115.1	s__Mycobacterium bacteremicum	80.1677	958	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	80.102	946	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001499995.1	s__Mycobacterium sp001499995	79.9747	883	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	79.9696	921	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	79.9073	885	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	79.7554	915	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004745805.1	s__Mycobacterium sp004745805	79.622	841	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250655.1	s__Mycobacterium sphagni	79.3055	793	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	79.2489	798	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	79.1759	709	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001667505.1	s__Mycobacterium sp001667505	79.1515	820	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157375.1	s__Mycobacterium rhizamassiliense	79.061	692	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667585.1	s__Mycobacterium sp001667585	78.8875	641	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	77.6486	416	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:11,682] [INFO] GTDB search result was written to GCF_010722995.1_ASM1072299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:11,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:11,686] [INFO] DFAST_QC result json was written to GCF_010722995.1_ASM1072299v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:11,686] [INFO] DFAST_QC completed!
[2024-01-24 12:18:11,686] [INFO] Total running time: 0h3m38s