[2024-01-24 10:57:25,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:25,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:25,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference
[2024-01-24 10:57:27,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,017] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg01c00971-0f3a-4aea-a25a-7902d2940f19/GCF_900232995.1_PRJEB22891_genomic.fna.gz | prodigal -d GCF_900232995.1_PRJEB22891_genomic.fna/cds.fna -a GCF_900232995.1_PRJEB22891_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:50,986] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:50,986] [INFO] Task started: HMMsearch
[2024-01-24 10:57:50,986] [INFO] Running command: hmmsearch --tblout GCF_900232995.1_PRJEB22891_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/reference_markers.hmm GCF_900232995.1_PRJEB22891_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:51,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:51,369] [INFO] Found 6/6 markers.
[2024-01-24 10:57:51,417] [INFO] Query marker FASTA was written to GCF_900232995.1_PRJEB22891_genomic.fna/markers.fasta
[2024-01-24 10:57:51,417] [INFO] Task started: Blastn
[2024-01-24 10:57:51,417] [INFO] Running command: blastn -query GCF_900232995.1_PRJEB22891_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/reference_markers.fasta -out GCF_900232995.1_PRJEB22891_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:52,487] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:52,490] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:52,490] [INFO] Target genome list was writen to GCF_900232995.1_PRJEB22891_genomic.fna/target_genomes.txt
[2024-01-24 10:57:52,529] [INFO] Task started: fastANI
[2024-01-24 10:57:52,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c00971-0f3a-4aea-a25a-7902d2940f19/GCF_900232995.1_PRJEB22891_genomic.fna.gz --refList GCF_900232995.1_PRJEB22891_genomic.fna/target_genomes.txt --output GCF_900232995.1_PRJEB22891_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:20,788] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:20,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:20,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:20,801] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:20,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:20,802] [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 simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	100.0	2014	2015	95	conclusive
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	91.6129	1588	2015	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	82.9058	1210	2015	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	82.8477	1252	2015	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	82.4884	1395	2015	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	82.3947	1391	2015	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	82.3106	1037	2015	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	82.2531	1099	2015	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	81.5158	1031	2015	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	81.3804	1149	2015	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	80.9568	1158	2015	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.9481	1081	2015	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.8322	1026	2015	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	80.689	1100	2015	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	80.6438	1095	2015	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	80.4228	1004	2015	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.4086	1020	2015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:20,803] [INFO] DFAST Taxonomy check result was written to GCF_900232995.1_PRJEB22891_genomic.fna/tc_result.tsv
[2024-01-24 10:58:20,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:20,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:20,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/checkm_data
[2024-01-24 10:58:20,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:20,861] [INFO] Task started: CheckM
[2024-01-24 10:58:20,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900232995.1_PRJEB22891_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900232995.1_PRJEB22891_genomic.fna/checkm_input GCF_900232995.1_PRJEB22891_genomic.fna/checkm_result
[2024-01-24 10:59:25,116] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:25,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:25,134] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:25,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:25,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900232995.1_PRJEB22891_genomic.fna/markers.fasta)
[2024-01-24 10:59:25,135] [INFO] Task started: Blastn
[2024-01-24 10:59:25,135] [INFO] Running command: blastn -query GCF_900232995.1_PRJEB22891_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b9b255-5e60-4bc9-bb60-23464ba956d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900232995.1_PRJEB22891_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:26,569] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:26,572] [INFO] Selected 19 target genomes.
[2024-01-24 10:59:26,572] [INFO] Target genome list was writen to GCF_900232995.1_PRJEB22891_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:26,618] [INFO] Task started: fastANI
[2024-01-24 10:59:26,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c00971-0f3a-4aea-a25a-7902d2940f19/GCF_900232995.1_PRJEB22891_genomic.fna.gz --refList GCF_900232995.1_PRJEB22891_genomic.fna/target_genomes_gtdb.txt --output GCF_900232995.1_PRJEB22891_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:52,988] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:53,003] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:53,003] [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_900232995.1	s__Mycobacterium simulans	100.0	2014	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	conclusive
GCF_002101845.1	s__Mycobacterium riyadhense	91.6069	1589	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_010731535.1	s__Mycobacterium lacus	82.8478	1254	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086155.1	s__Mycobacterium angelicum	82.4857	1395	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	82.2355	1101	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002104675.1	s__Mycobacterium decipiens	81.8511	1158	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730745.1	s__Mycobacterium heidelbergense	81.6469	1050	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102175.1	s__Mycobacterium gastri	81.3809	1149	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900566055.1	s__Mycobacterium innocens	81.3156	1113	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_001673535.1	s__Mycobacterium sp001673535	81.0171	1058	2015	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	80.9744	1077	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.9336	1056	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	80.9296	1166	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002101785.1	s__Mycobacterium palustre	80.8237	1027	2015	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	80.7625	1070	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667115.1	s__Mycobacterium sp001667115	80.6744	1023	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730195.1	s__Mycobacterium conspicuum	80.671	1104	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	80.5788	1014	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_010723575.1	s__Mycobacterium bourgelatii	80.5095	1118	2015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:53,005] [INFO] GTDB search result was written to GCF_900232995.1_PRJEB22891_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:53,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:53,009] [INFO] DFAST_QC result json was written to GCF_900232995.1_PRJEB22891_genomic.fna/dqc_result.json
[2024-01-24 10:59:53,009] [INFO] DFAST_QC completed!
[2024-01-24 10:59:53,010] [INFO] Total running time: 0h2m27s