[2024-01-24 13:57:13,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,361] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference
[2024-01-24 13:57:14,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,626] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c897ce8-3ea7-46a7-acc3-961fffdc4fc4/GCF_002101705.1_ASM210170v1_genomic.fna.gz | prodigal -d GCF_002101705.1_ASM210170v1_genomic.fna/cds.fna -a GCF_002101705.1_ASM210170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:34,121] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:34,121] [INFO] Task started: HMMsearch
[2024-01-24 13:57:34,121] [INFO] Running command: hmmsearch --tblout GCF_002101705.1_ASM210170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/reference_markers.hmm GCF_002101705.1_ASM210170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:34,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:34,462] [INFO] Found 6/6 markers.
[2024-01-24 13:57:34,519] [INFO] Query marker FASTA was written to GCF_002101705.1_ASM210170v1_genomic.fna/markers.fasta
[2024-01-24 13:57:34,520] [INFO] Task started: Blastn
[2024-01-24 13:57:34,520] [INFO] Running command: blastn -query GCF_002101705.1_ASM210170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/reference_markers.fasta -out GCF_002101705.1_ASM210170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:35,733] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:35,736] [INFO] Selected 23 target genomes.
[2024-01-24 13:57:35,737] [INFO] Target genome list was writen to GCF_002101705.1_ASM210170v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:35,749] [INFO] Task started: fastANI
[2024-01-24 13:57:35,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c897ce8-3ea7-46a7-acc3-961fffdc4fc4/GCF_002101705.1_ASM210170v1_genomic.fna.gz --refList GCF_002101705.1_ASM210170v1_genomic.fna/target_genomes.txt --output GCF_002101705.1_ASM210170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:05,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:05,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:05,906] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:05,906] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:05,906] [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 vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.0868	1127	2068	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	81.9628	1233	2068	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.8714	1364	2068	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.8688	1368	2068	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	81.6792	1247	2068	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.6607	1258	2068	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	81.3755	1136	2068	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.7357	1007	2068	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.7256	1003	2068	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.6378	1023	2068	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.3024	1000	2068	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.243	1002	2068	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.2395	1002	2068	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	79.6505	849	2068	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.4264	892	2068	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.4104	889	2068	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.3581	806	2068	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	79.2973	815	2068	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.2198	809	2068	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.1967	853	2068	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.1915	810	2068	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.0106	780	2068	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	78.6053	770	2068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,908] [INFO] DFAST Taxonomy check result was written to GCF_002101705.1_ASM210170v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:05,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:05,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:05,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/checkm_data
[2024-01-24 13:58:05,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:05,966] [INFO] Task started: CheckM
[2024-01-24 13:58:05,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101705.1_ASM210170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101705.1_ASM210170v1_genomic.fna/checkm_input GCF_002101705.1_ASM210170v1_genomic.fna/checkm_result
[2024-01-24 13:59:04,998] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:04,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,019] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:05,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:05,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101705.1_ASM210170v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:05,020] [INFO] Task started: Blastn
[2024-01-24 13:59:05,020] [INFO] Running command: blastn -query GCF_002101705.1_ASM210170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b9dd78-3f21-478c-9f7e-0e4c2f7eab1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101705.1_ASM210170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,928] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:06,929] [INFO] Target genome list was writen to GCF_002101705.1_ASM210170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:06,955] [INFO] Task started: fastANI
[2024-01-24 13:59:06,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c897ce8-3ea7-46a7-acc3-961fffdc4fc4/GCF_002101705.1_ASM210170v1_genomic.fna.gz --refList GCF_002101705.1_ASM210170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101705.1_ASM210170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:29,229] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:29,255] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:29,256] [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_002101705.1	s__Mycobacterium iranicum	100.0	2065	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	98.48	0.91	0.91	2	conclusive
GCF_001650495.1	s__Mycobacterium iranicum_A	89.6239	1659	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190915.1	s__Mycobacterium iranicum_B	82.6075	1343	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.5047	1059	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	82.4537	1341	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_900454025.1	s__Mycobacterium gilvum	82.3161	1278	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.2408	1322	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010725485.1	s__Mycobacterium sp002946335	82.2269	1311	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.5735	1217	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	80.73	1003	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001500125.1	s__Mycobacterium sp001500125	80.3739	949	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722355.1	s__Mycobacterium holsaticum	79.692	810	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	79.5443	870	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	79.4316	892	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_001494595.1	s__Mycobacterium sp001494595	79.4051	787	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295855.1	s__Mycobacterium fortuitum	79.3054	803	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_002592005.1	s__Mycobacterium palauense	79.2834	818	2068	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 13:59:29,257] [INFO] GTDB search result was written to GCF_002101705.1_ASM210170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:29,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:29,264] [INFO] DFAST_QC result json was written to GCF_002101705.1_ASM210170v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:29,265] [INFO] DFAST_QC completed!
[2024-01-24 13:59:29,265] [INFO] Total running time: 0h2m16s