[2024-01-25 19:50:50,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference
[2024-01-25 19:50:51,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,674] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg534f47b9-01fb-4537-bba4-a1f5961b1830/GCF_022558565.1_ASM2255856v1_genomic.fna.gz | prodigal -d GCF_022558565.1_ASM2255856v1_genomic.fna/cds.fna -a GCF_022558565.1_ASM2255856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:08,146] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:08,147] [INFO] Task started: HMMsearch
[2024-01-25 19:51:08,147] [INFO] Running command: hmmsearch --tblout GCF_022558565.1_ASM2255856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/reference_markers.hmm GCF_022558565.1_ASM2255856v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:08,406] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:08,407] [INFO] Found 6/6 markers.
[2024-01-25 19:51:08,453] [INFO] Query marker FASTA was written to GCF_022558565.1_ASM2255856v1_genomic.fna/markers.fasta
[2024-01-25 19:51:08,454] [INFO] Task started: Blastn
[2024-01-25 19:51:08,454] [INFO] Running command: blastn -query GCF_022558565.1_ASM2255856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/reference_markers.fasta -out GCF_022558565.1_ASM2255856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:09,494] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:09,497] [INFO] Selected 26 target genomes.
[2024-01-25 19:51:09,497] [INFO] Target genome list was writen to GCF_022558565.1_ASM2255856v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:09,511] [INFO] Task started: fastANI
[2024-01-25 19:51:09,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg534f47b9-01fb-4537-bba4-a1f5961b1830/GCF_022558565.1_ASM2255856v1_genomic.fna.gz --refList GCF_022558565.1_ASM2255856v1_genomic.fna/target_genomes.txt --output GCF_022558565.1_ASM2255856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:39,693] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:39,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:39,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:39,710] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:51:39,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:51:39,710] [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 elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	87.134	1431	1874	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	87.0403	1450	1874	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	82.6163	1178	1874	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.5565	1128	1874	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.5153	1151	1874	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.5138	1140	1874	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	82.2772	1175	1874	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	82.1491	1160	1874	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	82.0708	1186	1874	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	81.4302	1065	1874	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	81.3619	1038	1874	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.8044	973	1874	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.672	956	1874	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.6353	953	1874	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	80.1032	794	1874	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	80.0861	780	1874	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0579	944	1874	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0485	971	1874	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	79.9942	614	1874	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	79.9086	786	1874	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.8952	892	1874	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	79.8943	897	1874	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8548	851	1874	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7528	873	1874	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.731	726	1874	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	78.4028	525	1874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:39,712] [INFO] DFAST Taxonomy check result was written to GCF_022558565.1_ASM2255856v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:39,712] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:39,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:39,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/checkm_data
[2024-01-25 19:51:39,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:39,765] [INFO] Task started: CheckM
[2024-01-25 19:51:39,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022558565.1_ASM2255856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022558565.1_ASM2255856v1_genomic.fna/checkm_input GCF_022558565.1_ASM2255856v1_genomic.fna/checkm_result
[2024-01-25 19:52:50,755] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:50,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:50,781] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:50,781] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:50,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022558565.1_ASM2255856v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:50,782] [INFO] Task started: Blastn
[2024-01-25 19:52:50,782] [INFO] Running command: blastn -query GCF_022558565.1_ASM2255856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87e581b-82ca-4589-957a-5259521906a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_022558565.1_ASM2255856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:52,423] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:52,427] [INFO] Selected 24 target genomes.
[2024-01-25 19:52:52,427] [INFO] Target genome list was writen to GCF_022558565.1_ASM2255856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:52,443] [INFO] Task started: fastANI
[2024-01-25 19:52:52,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg534f47b9-01fb-4537-bba4-a1f5961b1830/GCF_022558565.1_ASM2255856v1_genomic.fna.gz --refList GCF_022558565.1_ASM2255856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022558565.1_ASM2255856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:23,696] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:23,710] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:23,711] [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_001722355.1	s__Mycobacterium holsaticum	98.7908	1531	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004014805.1	s__Mycobacterium elephantis	87.1688	1427	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_010725725.1	s__Mycobacterium pulveris	87.0287	1451	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	82.6262	1179	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	82.6202	1207	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	82.5441	1146	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001050015.1	s__Mycobacterium malmesburyense	82.2858	1172	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	82.1326	1195	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001570485.1	s__Mycobacterium novocastrense	81.998	1186	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_003284965.1	s__Mycobacterium sp003284965	81.854	1102	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668575.1	s__Mycobacterium sp001668575	81.7974	1172	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499905.1	s__Mycobacterium sp001499905	81.7433	1109	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240945.1	s__Mycobacterium sp900240945	81.2774	1110	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	81.0354	1079	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	80.737	1062	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_000266905.1	s__Mycobacterium chubuense_A	80.7226	999	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	80.3259	959	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101735.1	s__Mycobacterium kyorinense	80.1203	792	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_010727475.1	s__Mycobacterium mageritense	80.0512	971	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_002101595.1	s__Mycobacterium celatum	79.9182	783	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086485.1	s__Mycobacterium aquaticum	79.8841	899	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007714205.1	s__Mycobacterium helveticum	79.7602	720	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	79.6135	739	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_000195955.2	s__Mycobacterium tuberculosis	78.4111	524	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:23,712] [INFO] GTDB search result was written to GCF_022558565.1_ASM2255856v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:23,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:23,716] [INFO] DFAST_QC result json was written to GCF_022558565.1_ASM2255856v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:23,717] [INFO] DFAST_QC completed!
[2024-01-25 19:53:23,717] [INFO] Total running time: 0h2m33s