[2024-01-24 13:40:28,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,825] [INFO] DQC Reference Directory: /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference
[2024-01-24 13:40:30,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:30,220] [INFO] Task started: Prodigal
[2024-01-24 13:40:30,221] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe6e785c-3e72-4574-b83b-132d3c623c60/GCF_002101875.1_ASM210187v1_genomic.fna.gz | prodigal -d GCF_002101875.1_ASM210187v1_genomic.fna/cds.fna -a GCF_002101875.1_ASM210187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:50,186] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:50,186] [INFO] Task started: HMMsearch
[2024-01-24 13:40:50,186] [INFO] Running command: hmmsearch --tblout GCF_002101875.1_ASM210187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/reference_markers.hmm GCF_002101875.1_ASM210187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:50,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:50,491] [INFO] Found 6/6 markers.
[2024-01-24 13:40:50,542] [INFO] Query marker FASTA was written to GCF_002101875.1_ASM210187v1_genomic.fna/markers.fasta
[2024-01-24 13:40:50,543] [INFO] Task started: Blastn
[2024-01-24 13:40:50,543] [INFO] Running command: blastn -query GCF_002101875.1_ASM210187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/reference_markers.fasta -out GCF_002101875.1_ASM210187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:51,687] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:51,691] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:51,691] [INFO] Target genome list was writen to GCF_002101875.1_ASM210187v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:51,697] [INFO] Task started: fastANI
[2024-01-24 13:40:51,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6e785c-3e72-4574-b83b-132d3c623c60/GCF_002101875.1_ASM210187v1_genomic.fna.gz --refList GCF_002101875.1_ASM210187v1_genomic.fna/target_genomes.txt --output GCF_002101875.1_ASM210187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:09,851] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:09,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:09,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:09,864] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:09,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:09,864] [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 saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	100.0	1922	1928	95	conclusive
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	99.9819	1928	1928	95	conclusive
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.992	1277	1928	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.8401	1226	1928	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.8264	1142	1928	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.8171	1126	1928	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.7584	1270	1928	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.3148	1246	1928	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	83.2431	1240	1928	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	83.1584	1222	1928	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	82.8192	1024	1928	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	82.8157	1136	1928	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	82.7981	1139	1928	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	82.7462	1146	1928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,878] [INFO] DFAST Taxonomy check result was written to GCF_002101875.1_ASM210187v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:09,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:09,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:09,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/checkm_data
[2024-01-24 13:41:09,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:09,941] [INFO] Task started: CheckM
[2024-01-24 13:41:09,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101875.1_ASM210187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101875.1_ASM210187v1_genomic.fna/checkm_input GCF_002101875.1_ASM210187v1_genomic.fna/checkm_result
[2024-01-24 13:42:06,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:06,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,897] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:06,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:06,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101875.1_ASM210187v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:06,898] [INFO] Task started: Blastn
[2024-01-24 13:42:06,898] [INFO] Running command: blastn -query GCF_002101875.1_ASM210187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8564620-6025-4ac5-8346-26d34a897bb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101875.1_ASM210187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:08,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:08,521] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:08,522] [INFO] Target genome list was writen to GCF_002101875.1_ASM210187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:08,576] [INFO] Task started: fastANI
[2024-01-24 13:42:08,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe6e785c-3e72-4574-b83b-132d3c623c60/GCF_002101875.1_ASM210187v1_genomic.fna.gz --refList GCF_002101875.1_ASM210187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101875.1_ASM210187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:32,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:33,014] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:33,015] [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_010729105.1	s__Mycobacterium saskatchewanense	99.9819	1928	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_902652685.1	s__Mycobacterium sp902652685	84.1854	1279	1928	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	83.8339	1228	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_002101815.1	s__Mycobacterium paraense	83.7103	1278	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.6542	1215	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668725.1	s__Mycobacterium sp001668725	83.6183	1277	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	83.4472	1276	1928	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	83.4323	1269	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	83.4155	1231	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667035.1	s__Mycobacterium sp001667035	83.3272	1220	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	83.3109	1210	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	83.2733	1245	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	83.2546	1245	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	83.2451	1244	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102255.1	s__Mycobacterium nebraskense	83.1583	1221	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_001666835.1	s__Mycobacterium sp001666835	83.0825	1175	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_010730575.1	s__Mycobacterium parmense	82.6976	1255	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001672755.1	s__Mycobacterium colombiense_C	82.4896	1159	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954275.1	s__Mycobacterium sp001954275	82.4443	1102	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:33,016] [INFO] GTDB search result was written to GCF_002101875.1_ASM210187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:33,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:33,021] [INFO] DFAST_QC result json was written to GCF_002101875.1_ASM210187v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:33,021] [INFO] DFAST_QC completed!
[2024-01-24 13:42:33,021] [INFO] Total running time: 0h2m4s