[2024-01-24 15:02:07,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference
[2024-01-24 15:02:09,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,599] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg16512f98-2ef6-4ea2-a445-2b96812e2f5a/GCF_025821545.1_ASM2582154v1_genomic.fna.gz | prodigal -d GCF_025821545.1_ASM2582154v1_genomic.fna/cds.fna -a GCF_025821545.1_ASM2582154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:34,011] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:34,011] [INFO] Task started: HMMsearch
[2024-01-24 15:02:34,011] [INFO] Running command: hmmsearch --tblout GCF_025821545.1_ASM2582154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/reference_markers.hmm GCF_025821545.1_ASM2582154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:34,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:34,299] [INFO] Found 6/6 markers.
[2024-01-24 15:02:34,367] [INFO] Query marker FASTA was written to GCF_025821545.1_ASM2582154v1_genomic.fna/markers.fasta
[2024-01-24 15:02:34,368] [INFO] Task started: Blastn
[2024-01-24 15:02:34,368] [INFO] Running command: blastn -query GCF_025821545.1_ASM2582154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/reference_markers.fasta -out GCF_025821545.1_ASM2582154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:35,576] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:35,579] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:35,580] [INFO] Target genome list was writen to GCF_025821545.1_ASM2582154v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:35,595] [INFO] Task started: fastANI
[2024-01-24 15:02:35,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg16512f98-2ef6-4ea2-a445-2b96812e2f5a/GCF_025821545.1_ASM2582154v1_genomic.fna.gz --refList GCF_025821545.1_ASM2582154v1_genomic.fna/target_genomes.txt --output GCF_025821545.1_ASM2582154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:06,800] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:06,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:06,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:06,819] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:06,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:06,820] [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 setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	99.9943	2077	2085	95	conclusive
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	88.1058	1696	2085	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	88.0981	1719	2085	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	88.0941	1696	2085	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	87.5524	1710	2085	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	87.5415	1716	2085	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	86.4882	1621	2085	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	86.4067	1707	2085	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	86.257	1527	2085	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	86.0685	1458	2085	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	85.8513	1617	2085	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	85.8085	1636	2085	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	85.768	1658	2085	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	85.022	1453	2085	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.0681	1332	2085	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.0581	1341	2085	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.459	850	2085	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.2146	863	2085	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.0793	794	2085	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.0489	875	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:06,822] [INFO] DFAST Taxonomy check result was written to GCF_025821545.1_ASM2582154v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:06,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:06,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:06,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/checkm_data
[2024-01-24 15:03:06,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:06,890] [INFO] Task started: CheckM
[2024-01-24 15:03:06,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821545.1_ASM2582154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821545.1_ASM2582154v1_genomic.fna/checkm_input GCF_025821545.1_ASM2582154v1_genomic.fna/checkm_result
[2024-01-24 15:04:27,583] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:27,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:27,603] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:27,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:27,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821545.1_ASM2582154v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:27,604] [INFO] Task started: Blastn
[2024-01-24 15:04:27,604] [INFO] Running command: blastn -query GCF_025821545.1_ASM2582154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg938b71a2-56b2-4309-b89f-ac8d5ab8f27b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821545.1_ASM2582154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:29,576] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:29,579] [INFO] Selected 16 target genomes.
[2024-01-24 15:04:29,580] [INFO] Target genome list was writen to GCF_025821545.1_ASM2582154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:29,592] [INFO] Task started: fastANI
[2024-01-24 15:04:29,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg16512f98-2ef6-4ea2-a445-2b96812e2f5a/GCF_025821545.1_ASM2582154v1_genomic.fna.gz --refList GCF_025821545.1_ASM2582154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821545.1_ASM2582154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:54,879] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:54,892] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:54,893] [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_000805385.1	s__Mycobacterium setense	99.9943	2077	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	conclusive
GCF_000426065.1	s__Mycobacterium sp000426065	91.2755	1850	2085	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	88.1009	1694	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004762045.1	s__Mycobacterium sp004762045	87.8801	1659	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	87.5646	1708	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001245615.1	s__Mycobacterium neworleansense	87.5516	1715	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	87.2803	1696	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_011745145.1	s__Mycobacterium sp011745145	86.7027	1627	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	86.4942	1623	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_009729095.1	s__Mycobacterium sp009729095	86.4905	1502	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_010727325.1	s__Mycobacterium alvei	86.0715	1457	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	85.8424	1619	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	85.0131	1455	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	82.0692	1332	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.0497	954	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_010729895.1	s__Mycobacterium confluentis	79.804	897	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:54,894] [INFO] GTDB search result was written to GCF_025821545.1_ASM2582154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:54,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:54,900] [INFO] DFAST_QC result json was written to GCF_025821545.1_ASM2582154v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:54,900] [INFO] DFAST_QC completed!
[2024-01-24 15:04:54,901] [INFO] Total running time: 0h2m47s