[2024-01-25 18:40:05,532] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference
[2024-01-25 18:40:06,701] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,702] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg3acf32a5-22a3-41a9-a0a8-2edea5dd18d6/GCF_021654635.1_ASM2165463v1_genomic.fna.gz | prodigal -d GCF_021654635.1_ASM2165463v1_genomic.fna/cds.fna -a GCF_021654635.1_ASM2165463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:24,555] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:24,555] [INFO] Task started: HMMsearch
[2024-01-25 18:40:24,555] [INFO] Running command: hmmsearch --tblout GCF_021654635.1_ASM2165463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/reference_markers.hmm GCF_021654635.1_ASM2165463v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:24,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:24,824] [INFO] Found 6/6 markers.
[2024-01-25 18:40:24,876] [INFO] Query marker FASTA was written to GCF_021654635.1_ASM2165463v1_genomic.fna/markers.fasta
[2024-01-25 18:40:24,876] [INFO] Task started: Blastn
[2024-01-25 18:40:24,876] [INFO] Running command: blastn -query GCF_021654635.1_ASM2165463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/reference_markers.fasta -out GCF_021654635.1_ASM2165463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:25,892] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:25,898] [INFO] Selected 15 target genomes.
[2024-01-25 18:40:25,898] [INFO] Target genome list was writen to GCF_021654635.1_ASM2165463v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:25,903] [INFO] Task started: fastANI
[2024-01-25 18:40:25,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg3acf32a5-22a3-41a9-a0a8-2edea5dd18d6/GCF_021654635.1_ASM2165463v1_genomic.fna.gz --refList GCF_021654635.1_ASM2165463v1_genomic.fna/target_genomes.txt --output GCF_021654635.1_ASM2165463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:47,478] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:47,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:47,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:47,488] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:40:47,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:40:47,489] [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 vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	86.7205	1522	2115	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	82.4318	1368	2115	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	82.405	1371	2115	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	82.2721	1300	2115	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	81.866	1261	2115	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	81.4609	962	2115	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.2314	1155	2115	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.2296	1071	2115	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	81.2256	1043	2115	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	81.1988	1013	2115	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	81.1103	980	2115	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.9946	1122	2115	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	80.8336	1043	2115	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	80.7882	1096	2115	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	80.7699	1002	2115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:47,491] [INFO] DFAST Taxonomy check result was written to GCF_021654635.1_ASM2165463v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:47,491] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:47,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:47,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/checkm_data
[2024-01-25 18:40:47,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:47,556] [INFO] Task started: CheckM
[2024-01-25 18:40:47,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654635.1_ASM2165463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654635.1_ASM2165463v1_genomic.fna/checkm_input GCF_021654635.1_ASM2165463v1_genomic.fna/checkm_result
[2024-01-25 18:41:44,922] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:44,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:44,941] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:44,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:44,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654635.1_ASM2165463v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:44,943] [INFO] Task started: Blastn
[2024-01-25 18:41:44,943] [INFO] Running command: blastn -query GCF_021654635.1_ASM2165463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb59582-d36b-4a0f-a497-e181344fbff6/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654635.1_ASM2165463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:46,469] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:46,471] [INFO] Selected 18 target genomes.
[2024-01-25 18:41:46,472] [INFO] Target genome list was writen to GCF_021654635.1_ASM2165463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:46,496] [INFO] Task started: fastANI
[2024-01-25 18:41:46,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg3acf32a5-22a3-41a9-a0a8-2edea5dd18d6/GCF_021654635.1_ASM2165463v1_genomic.fna.gz --refList GCF_021654635.1_ASM2165463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654635.1_ASM2165463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:13,627] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:13,638] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:13,638] [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_013466425.1	s__Mycobacterium vicinigordonae	86.7486	1518	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417955.2	s__Mycobacterium gordonae_B	82.4725	1326	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	82.4509	1360	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCA_003987775.1	s__Mycobacterium sp003987775	82.302	1328	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101675.1	s__Mycobacterium gordonae	82.265	1302	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	82.0493	1203	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086405.1	s__Mycobacterium gordonae_D	81.9328	1296	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673365.1	s__Mycobacterium asiaticum_A	81.7714	1201	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	81.4946	1100	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	81.4354	1095	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	81.4033	1129	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673315.1	s__Mycobacterium asiaticum_B	81.3373	1167	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	81.2296	1154	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	81.2038	1012	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_002116635.1	s__Mycobacterium szulgai	80.988	1121	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	80.82	1090	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002102355.1	s__Mycobacterium sherrisii	80.768	1003	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	-
GCF_008370645.1	s__Mycobacterium simiae_A	79.7541	784	2115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:13,640] [INFO] GTDB search result was written to GCF_021654635.1_ASM2165463v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:13,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:13,644] [INFO] DFAST_QC result json was written to GCF_021654635.1_ASM2165463v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:13,644] [INFO] DFAST_QC completed!
[2024-01-25 18:42:13,644] [INFO] Total running time: 0h2m8s