[2024-01-25 19:50:35,497] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference
[2024-01-25 19:50:36,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:36,671] [INFO] Task started: Prodigal
[2024-01-25 19:50:36,671] [INFO] Running command: gunzip -c /var/lib/cwl/stga8e71596-868f-4b47-bea6-925fd7cb6f2d/GCF_022558525.1_ASM2255852v1_genomic.fna.gz | prodigal -d GCF_022558525.1_ASM2255852v1_genomic.fna/cds.fna -a GCF_022558525.1_ASM2255852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:17,179] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:17,179] [INFO] Task started: HMMsearch
[2024-01-25 19:51:17,179] [INFO] Running command: hmmsearch --tblout GCF_022558525.1_ASM2255852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/reference_markers.hmm GCF_022558525.1_ASM2255852v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:17,445] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:17,446] [INFO] Found 6/6 markers.
[2024-01-25 19:51:17,498] [INFO] Query marker FASTA was written to GCF_022558525.1_ASM2255852v1_genomic.fna/markers.fasta
[2024-01-25 19:51:17,498] [INFO] Task started: Blastn
[2024-01-25 19:51:17,498] [INFO] Running command: blastn -query GCF_022558525.1_ASM2255852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/reference_markers.fasta -out GCF_022558525.1_ASM2255852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:18,734] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:18,736] [INFO] Selected 15 target genomes.
[2024-01-25 19:51:18,737] [INFO] Target genome list was writen to GCF_022558525.1_ASM2255852v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:18,743] [INFO] Task started: fastANI
[2024-01-25 19:51:18,744] [INFO] Running command: fastANI --query /var/lib/cwl/stga8e71596-868f-4b47-bea6-925fd7cb6f2d/GCF_022558525.1_ASM2255852v1_genomic.fna.gz --refList GCF_022558525.1_ASM2255852v1_genomic.fna/target_genomes.txt --output GCF_022558525.1_ASM2255852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:42,645] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:42,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:42,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:42,656] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:42,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:42,656] [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 boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	99.9986	2180	2180	95	conclusive
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	89.2223	1795	2180	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	89.1493	1809	2180	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	89.1478	1828	2180	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	88.5112	1802	2180	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	88.3864	1689	2180	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	87.5758	1697	2180	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	86.9186	1695	2180	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	86.7942	1559	2180	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	86.7854	1515	2180	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	86.4582	1661	2180	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8837	865	2180	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.737	906	2180	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6662	912	2180	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.547	915	2180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:42,658] [INFO] DFAST Taxonomy check result was written to GCF_022558525.1_ASM2255852v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:42,658] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:42,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:42,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/checkm_data
[2024-01-25 19:51:42,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:42,722] [INFO] Task started: CheckM
[2024-01-25 19:51:42,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022558525.1_ASM2255852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022558525.1_ASM2255852v1_genomic.fna/checkm_input GCF_022558525.1_ASM2255852v1_genomic.fna/checkm_result
[2024-01-25 19:54:03,953] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:03,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:03,970] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:03,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:03,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022558525.1_ASM2255852v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:03,972] [INFO] Task started: Blastn
[2024-01-25 19:54:03,972] [INFO] Running command: blastn -query GCF_022558525.1_ASM2255852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e6f4a10-c705-44a5-be1e-19ea65fc27e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_022558525.1_ASM2255852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:06,038] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:06,041] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:06,041] [INFO] Target genome list was writen to GCF_022558525.1_ASM2255852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:06,051] [INFO] Task started: fastANI
[2024-01-25 19:54:06,051] [INFO] Running command: fastANI --query /var/lib/cwl/stga8e71596-868f-4b47-bea6-925fd7cb6f2d/GCF_022558525.1_ASM2255852v1_genomic.fna.gz --refList GCF_022558525.1_ASM2255852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022558525.1_ASM2255852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:23,870] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:23,878] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:23,878] [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_010731295.1	s__Mycobacterium boenickei	99.9986	2180	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	conclusive
GCF_002086835.1	s__Mycobacterium porcinum	92.9945	1912	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001942045.1	s__Mycobacterium porcinum_A	92.8591	1773	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	89.1559	1808	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004762045.1	s__Mycobacterium sp004762045	89.0942	1742	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001245615.1	s__Mycobacterium neworleansense	88.5191	1801	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723385.1	s__Mycobacterium farcinogenes	88.299	1687	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	88.1863	1644	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_010727325.1	s__Mycobacterium alvei	86.7918	1514	2180	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	86.7298	1559	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_900078665.2	s__Mycobacterium houstonense	86.4516	1662	2180	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 19:54:23,880] [INFO] GTDB search result was written to GCF_022558525.1_ASM2255852v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:23,880] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:23,883] [INFO] DFAST_QC result json was written to GCF_022558525.1_ASM2255852v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:23,883] [INFO] DFAST_QC completed!
[2024-01-25 19:54:23,883] [INFO] Total running time: 0h3m48s