[2024-01-24 13:49:55,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference
[2024-01-24 13:49:56,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,500] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg93ec1625-3404-4023-9b7d-be5c3eac0b1e/GCF_002102155.1_ASM210215v1_genomic.fna.gz | prodigal -d GCF_002102155.1_ASM210215v1_genomic.fna/cds.fna -a GCF_002102155.1_ASM210215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:13,581] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:13,582] [INFO] Task started: HMMsearch
[2024-01-24 13:50:13,582] [INFO] Running command: hmmsearch --tblout GCF_002102155.1_ASM210215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/reference_markers.hmm GCF_002102155.1_ASM210215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:13,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:13,877] [INFO] Found 6/6 markers.
[2024-01-24 13:50:13,931] [INFO] Query marker FASTA was written to GCF_002102155.1_ASM210215v1_genomic.fna/markers.fasta
[2024-01-24 13:50:13,931] [INFO] Task started: Blastn
[2024-01-24 13:50:13,932] [INFO] Running command: blastn -query GCF_002102155.1_ASM210215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/reference_markers.fasta -out GCF_002102155.1_ASM210215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:15,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:15,142] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:15,143] [INFO] Target genome list was writen to GCF_002102155.1_ASM210215v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:15,204] [INFO] Task started: fastANI
[2024-01-24 13:50:15,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg93ec1625-3404-4023-9b7d-be5c3eac0b1e/GCF_002102155.1_ASM210215v1_genomic.fna.gz --refList GCF_002102155.1_ASM210215v1_genomic.fna/target_genomes.txt --output GCF_002102155.1_ASM210215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:37,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:37,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:37,248] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:37,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:37,248] [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 seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	89.8129	1526	1843	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	89.571	1543	1843	95	below_threshold
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	89.5329	1497	1843	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	88.8383	1473	1843	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	84.7869	1187	1843	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.7314	1292	1843	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	84.4905	1140	1843	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	84.3769	1304	1843	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.3727	1170	1843	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	84.2358	1336	1843	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	84.224	1411	1843	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	83.7157	1214	1843	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.6119	1254	1843	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	83.4325	1131	1843	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	82.7221	1199	1843	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	82.6419	1199	1843	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	82.5227	1101	1843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,250] [INFO] DFAST Taxonomy check result was written to GCF_002102155.1_ASM210215v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:37,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:37,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:37,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/checkm_data
[2024-01-24 13:50:37,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:37,306] [INFO] Task started: CheckM
[2024-01-24 13:50:37,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102155.1_ASM210215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102155.1_ASM210215v1_genomic.fna/checkm_input GCF_002102155.1_ASM210215v1_genomic.fna/checkm_result
[2024-01-24 13:51:29,100] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:29,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:29,121] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:29,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:29,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102155.1_ASM210215v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:29,123] [INFO] Task started: Blastn
[2024-01-24 13:51:29,123] [INFO] Running command: blastn -query GCF_002102155.1_ASM210215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3853329f-ff5b-4175-b6d9-7d2b4fa68476/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102155.1_ASM210215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:30,917] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:30,922] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:30,922] [INFO] Target genome list was writen to GCF_002102155.1_ASM210215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:30,954] [INFO] Task started: fastANI
[2024-01-24 13:51:30,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg93ec1625-3404-4023-9b7d-be5c3eac0b1e/GCF_002102155.1_ASM210215v1_genomic.fna.gz --refList GCF_002102155.1_ASM210215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102155.1_ASM210215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:50,607] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:50,626] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:50,627] [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_002102155.1	s__Mycobacterium europaeum	100.0	1837	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	conclusive
GCF_900240975.1	s__Mycobacterium sp900240975	91.895	1568	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_010731595.1	s__Mycobacterium seoulense	89.8164	1525	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731655.1	s__Mycobacterium paraseoulense	89.5612	1544	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102255.1	s__Mycobacterium nebraskense	88.8382	1472	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	88.528	1506	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	88.4418	1554	1843	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	88.3184	1441	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_001667885.1	s__Mycobacterium scrofulaceum_C	87.859	1424	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.31	98.31	0.93	0.93	2	-
GCF_001667275.1	s__Mycobacterium sp001667275	87.8494	1420	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001907675.1	s__Mycobacterium paraffinicum	87.5188	1452	1843	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	84.7314	1292	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_002101815.1	s__Mycobacterium paraense	84.362	1306	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCA_002291465.1	s__Mycobacterium lepraemurium	84.3239	1107	1843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:50,629] [INFO] GTDB search result was written to GCF_002102155.1_ASM210215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:50,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:50,633] [INFO] DFAST_QC result json was written to GCF_002102155.1_ASM210215v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:50,634] [INFO] DFAST_QC completed!
[2024-01-24 13:51:50,634] [INFO] Total running time: 0h1m55s