[2024-01-24 12:34:20,579] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,581] [INFO] DQC Reference Directory: /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference
[2024-01-24 12:34:21,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,772] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg66b794ea-e079-47e4-9d0e-f7da5d82f77c/GCF_900157385.1_PRJEB19184_genomic.fna.gz | prodigal -d GCF_900157385.1_PRJEB19184_genomic.fna/cds.fna -a GCF_900157385.1_PRJEB19184_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:40,240] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:40,241] [INFO] Task started: HMMsearch
[2024-01-24 12:34:40,241] [INFO] Running command: hmmsearch --tblout GCF_900157385.1_PRJEB19184_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/reference_markers.hmm GCF_900157385.1_PRJEB19184_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:40,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:40,533] [INFO] Found 6/6 markers.
[2024-01-24 12:34:40,584] [INFO] Query marker FASTA was written to GCF_900157385.1_PRJEB19184_genomic.fna/markers.fasta
[2024-01-24 12:34:40,585] [INFO] Task started: Blastn
[2024-01-24 12:34:40,585] [INFO] Running command: blastn -query GCF_900157385.1_PRJEB19184_genomic.fna/markers.fasta -db /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/reference_markers.fasta -out GCF_900157385.1_PRJEB19184_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:41,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:41,747] [INFO] Selected 17 target genomes.
[2024-01-24 12:34:41,747] [INFO] Target genome list was writen to GCF_900157385.1_PRJEB19184_genomic.fna/target_genomes.txt
[2024-01-24 12:34:41,753] [INFO] Task started: fastANI
[2024-01-24 12:34:41,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b794ea-e079-47e4-9d0e-f7da5d82f77c/GCF_900157385.1_PRJEB19184_genomic.fna.gz --refList GCF_900157385.1_PRJEB19184_genomic.fna/target_genomes.txt --output GCF_900157385.1_PRJEB19184_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:35:03,196] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:03,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:35:03,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:35:03,214] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:35:03,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:35:03,215] [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 paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	91.4728	1638	2005	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	86.0286	1270	2005	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	86.0034	1302	2005	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.3409	1359	2005	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.8894	1374	2005	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.8552	1289	2005	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	83.6574	1296	2005	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.5948	1266	2005	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.5726	1294	2005	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	83.346	1274	2005	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.3434	1321	2005	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.3298	1341	2005	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	83.3066	1246	2005	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	81.1856	1071	2005	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	81.1659	1066	2005	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	81.1207	1088	2005	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.913	1100	2005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:35:03,216] [INFO] DFAST Taxonomy check result was written to GCF_900157385.1_PRJEB19184_genomic.fna/tc_result.tsv
[2024-01-24 12:35:03,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:35:03,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:35:03,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/checkm_data
[2024-01-24 12:35:03,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:35:03,280] [INFO] Task started: CheckM
[2024-01-24 12:35:03,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900157385.1_PRJEB19184_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900157385.1_PRJEB19184_genomic.fna/checkm_input GCF_900157385.1_PRJEB19184_genomic.fna/checkm_result
[2024-01-24 12:35:58,284] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:58,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:58,307] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:58,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:58,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900157385.1_PRJEB19184_genomic.fna/markers.fasta)
[2024-01-24 12:35:58,308] [INFO] Task started: Blastn
[2024-01-24 12:35:58,308] [INFO] Running command: blastn -query GCF_900157385.1_PRJEB19184_genomic.fna/markers.fasta -db /var/lib/cwl/stge36ea3ea-a760-4317-bddb-b709fe00dacd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900157385.1_PRJEB19184_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:59,956] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:59,960] [INFO] Selected 10 target genomes.
[2024-01-24 12:35:59,960] [INFO] Target genome list was writen to GCF_900157385.1_PRJEB19184_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:59,969] [INFO] Task started: fastANI
[2024-01-24 12:35:59,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b794ea-e079-47e4-9d0e-f7da5d82f77c/GCF_900157385.1_PRJEB19184_genomic.fna.gz --refList GCF_900157385.1_PRJEB19184_genomic.fna/target_genomes_gtdb.txt --output GCF_900157385.1_PRJEB19184_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:15,408] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:15,427] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:15,427] [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_900157385.1	s__Mycobacterium terramassiliense	100.0	1989	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002102225.1	s__Mycobacterium interjectum_B	94.5063	1726	2005	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	93.4889	1653	2005	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	92.1268	1580	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	91.4624	1639	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	91.3296	1575	2005	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	89.0502	1571	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	87.3343	1499	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672815.1	s__Mycobacterium sp001672815	86.7184	1470	2005	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	83.8504	1288	2005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:15,429] [INFO] GTDB search result was written to GCF_900157385.1_PRJEB19184_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:15,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:15,435] [INFO] DFAST_QC result json was written to GCF_900157385.1_PRJEB19184_genomic.fna/dqc_result.json
[2024-01-24 12:36:15,435] [INFO] DFAST_QC completed!
[2024-01-24 12:36:15,435] [INFO] Total running time: 0h1m55s