[2024-01-25 17:34:07,121] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference
[2024-01-25 17:34:09,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,026] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg956a6c88-2b1f-4eb9-b166-83abaaee9fab/GCF_025821345.1_ASM2582134v1_genomic.fna.gz | prodigal -d GCF_025821345.1_ASM2582134v1_genomic.fna/cds.fna -a GCF_025821345.1_ASM2582134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:27,606] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:27,606] [INFO] Task started: HMMsearch
[2024-01-25 17:34:27,606] [INFO] Running command: hmmsearch --tblout GCF_025821345.1_ASM2582134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/reference_markers.hmm GCF_025821345.1_ASM2582134v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:27,925] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:27,926] [INFO] Found 6/6 markers.
[2024-01-25 17:34:27,978] [INFO] Query marker FASTA was written to GCF_025821345.1_ASM2582134v1_genomic.fna/markers.fasta
[2024-01-25 17:34:27,979] [INFO] Task started: Blastn
[2024-01-25 17:34:27,979] [INFO] Running command: blastn -query GCF_025821345.1_ASM2582134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/reference_markers.fasta -out GCF_025821345.1_ASM2582134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:29,074] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:29,077] [INFO] Selected 14 target genomes.
[2024-01-25 17:34:29,077] [INFO] Target genome list was writen to GCF_025821345.1_ASM2582134v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:29,080] [INFO] Task started: fastANI
[2024-01-25 17:34:29,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg956a6c88-2b1f-4eb9-b166-83abaaee9fab/GCF_025821345.1_ASM2582134v1_genomic.fna.gz --refList GCF_025821345.1_ASM2582134v1_genomic.fna/target_genomes.txt --output GCF_025821345.1_ASM2582134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:48,470] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:48,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:48,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:48,480] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:48,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:48,481] [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
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	99.9972	1981	1985	95	conclusive
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	99.9867	1969	1985	95	conclusive
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.5375	1213	1985	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	82.3874	1356	1985	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	81.9295	1307	1985	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.919	1265	1985	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.8894	1326	1985	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.7042	1046	1985	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	79.87	1053	1985	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.8189	1049	1985	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.4259	821	1985	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.4026	871	1985	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.325	859	1985	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.2981	872	1985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:48,482] [INFO] DFAST Taxonomy check result was written to GCF_025821345.1_ASM2582134v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:48,483] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:48,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:48,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/checkm_data
[2024-01-25 17:34:48,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:48,539] [INFO] Task started: CheckM
[2024-01-25 17:34:48,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821345.1_ASM2582134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821345.1_ASM2582134v1_genomic.fna/checkm_input GCF_025821345.1_ASM2582134v1_genomic.fna/checkm_result
[2024-01-25 17:35:48,721] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:48,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:48,757] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:48,758] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:48,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821345.1_ASM2582134v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:48,759] [INFO] Task started: Blastn
[2024-01-25 17:35:48,759] [INFO] Running command: blastn -query GCF_025821345.1_ASM2582134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc34eb787-e1c5-45d9-b057-5408ee56d8d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821345.1_ASM2582134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:50,619] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:50,623] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:50,623] [INFO] Target genome list was writen to GCF_025821345.1_ASM2582134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:50,636] [INFO] Task started: fastANI
[2024-01-25 17:35:50,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg956a6c88-2b1f-4eb9-b166-83abaaee9fab/GCF_025821345.1_ASM2582134v1_genomic.fna.gz --refList GCF_025821345.1_ASM2582134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821345.1_ASM2582134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:25,260] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:25,273] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:25,273] [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_900637195.1	s__Mycobacterium aurum	99.9972	1981	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000612725.1	s__Mycobacterium austroafricanum	82.7723	1342	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.5977	1099	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	82.5397	1213	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.3805	1345	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014190915.1	s__Mycobacterium iranicum_B	82.3503	1338	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454025.1	s__Mycobacterium gilvum	82.2575	1300	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_001044255.1	s__Mycobacterium chubuense	81.9337	1255	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	81.9162	1311	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.8692	1262	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101705.1	s__Mycobacterium iranicum	81.8096	1346	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	98.48	0.91	0.91	2	-
GCF_005222675.1	s__Mycobacterium sp005222675	81.7884	1224	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	81.701	1201	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	81.6486	1241	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	81.4973	1216	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	81.1494	1104	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_010728325.1	s__Mycobacterium poriferae	80.9102	1202	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.01	98.01	0.88	0.88	2	-
GCF_010731735.1	s__Mycobacterium sediminis	79.9336	1021	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	79.8766	1053	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428895.1	s__Mycobacterium sp001428895	79.8651	1018	1985	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329585.1	s__Mycobacterium sp008329585	79.5845	1003	1985	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 17:36:25,275] [INFO] GTDB search result was written to GCF_025821345.1_ASM2582134v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:25,275] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:25,279] [INFO] DFAST_QC result json was written to GCF_025821345.1_ASM2582134v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:25,279] [INFO] DFAST_QC completed!
[2024-01-25 17:36:25,279] [INFO] Total running time: 0h2m18s