[2024-01-25 18:52:20,704] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference
[2024-01-25 18:52:21,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,857] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg80cf7e8b-8e35-48fc-9809-6e3682809716/GCF_025822065.1_ASM2582206v1_genomic.fna.gz | prodigal -d GCF_025822065.1_ASM2582206v1_genomic.fna/cds.fna -a GCF_025822065.1_ASM2582206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:43,712] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:43,712] [INFO] Task started: HMMsearch
[2024-01-25 18:52:43,712] [INFO] Running command: hmmsearch --tblout GCF_025822065.1_ASM2582206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/reference_markers.hmm GCF_025822065.1_ASM2582206v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:44,050] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:44,051] [INFO] Found 6/6 markers.
[2024-01-25 18:52:44,104] [INFO] Query marker FASTA was written to GCF_025822065.1_ASM2582206v1_genomic.fna/markers.fasta
[2024-01-25 18:52:44,105] [INFO] Task started: Blastn
[2024-01-25 18:52:44,105] [INFO] Running command: blastn -query GCF_025822065.1_ASM2582206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/reference_markers.fasta -out GCF_025822065.1_ASM2582206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:45,110] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:45,113] [INFO] Selected 25 target genomes.
[2024-01-25 18:52:45,114] [INFO] Target genome list was writen to GCF_025822065.1_ASM2582206v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:45,126] [INFO] Task started: fastANI
[2024-01-25 18:52:45,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cf7e8b-8e35-48fc-9809-6e3682809716/GCF_025822065.1_ASM2582206v1_genomic.fna.gz --refList GCF_025822065.1_ASM2582206v1_genomic.fna/target_genomes.txt --output GCF_025822065.1_ASM2582206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:21,801] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:21,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:21,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:21,816] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:53:21,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:53:21,817] [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 shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	80.9346	902	2249	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	80.9166	951	2249	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.7783	1105	2249	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.777	1183	2249	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.6763	1038	2249	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.6612	1160	2249	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.5918	1227	2249	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.5177	1215	2249	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	80.5159	1152	2249	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.4047	991	2249	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	80.3807	1183	2249	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	80.369	1125	2249	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	80.3389	1062	2249	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	80.3213	1111	2249	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.317	1196	2249	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.3124	1113	2249	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	80.3072	943	2249	95	below_threshold
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	80.2122	1095	2249	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.1894	1004	2249	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	80.0336	845	2249	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.354	659	2249	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	78.3516	617	2249	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.3069	653	2249	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	78.1909	596	2249	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	78.068	646	2249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:21,818] [INFO] DFAST Taxonomy check result was written to GCF_025822065.1_ASM2582206v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:21,818] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:21,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:21,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/checkm_data
[2024-01-25 18:53:21,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:21,893] [INFO] Task started: CheckM
[2024-01-25 18:53:21,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822065.1_ASM2582206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822065.1_ASM2582206v1_genomic.fna/checkm_input GCF_025822065.1_ASM2582206v1_genomic.fna/checkm_result
[2024-01-25 18:54:26,453] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:26,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:26,474] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:26,474] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:26,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822065.1_ASM2582206v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:26,476] [INFO] Task started: Blastn
[2024-01-25 18:54:26,476] [INFO] Running command: blastn -query GCF_025822065.1_ASM2582206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e233d8-fda4-47b2-9d98-24ad0ef57c1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822065.1_ASM2582206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:27,983] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:27,987] [INFO] Selected 19 target genomes.
[2024-01-25 18:54:27,987] [INFO] Target genome list was writen to GCF_025822065.1_ASM2582206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:27,998] [INFO] Task started: fastANI
[2024-01-25 18:54:27,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cf7e8b-8e35-48fc-9809-6e3682809716/GCF_025822065.1_ASM2582206v1_genomic.fna.gz --refList GCF_025822065.1_ASM2582206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822065.1_ASM2582206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:57,927] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:57,939] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:57,940] [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_002086275.1	s__Mycobacterium intermedium	99.9145	2088	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	conclusive
GCF_010723575.1	s__Mycobacterium bourgelatii	91.9377	2000	2249	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	80.9243	950	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002086155.1	s__Mycobacterium angelicum	80.8153	1179	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	80.6535	1134	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	80.6231	1160	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.5953	1230	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.4939	1098	2249	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	80.4847	1113	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613245.1	s__Mycobacterium asiaticum	80.3861	1180	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.3471	1060	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.3147	941	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_002086675.1	s__Mycobacterium persicum	80.2345	996	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCA_019247635.1	s__Mycobacterium sp019247635	80.2096	893	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673155.1	s__Mycobacterium sp001673155	80.2085	924	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104675.1	s__Mycobacterium decipiens	80.0961	959	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382405.1	s__Mycobacterium sp000382405	78.2568	496	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729095.1	s__Mycobacterium sp009729095	78.231	655	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_013390125.1	s__Mycobacterium hippocampi_A	78.1864	581	2249	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 18:54:57,941] [INFO] GTDB search result was written to GCF_025822065.1_ASM2582206v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:57,941] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:57,945] [INFO] DFAST_QC result json was written to GCF_025822065.1_ASM2582206v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:57,945] [INFO] DFAST_QC completed!
[2024-01-25 18:54:57,945] [INFO] Total running time: 0h2m37s