[2024-01-24 15:03:29,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference
[2024-01-24 15:03:30,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:30,460] [INFO] Task started: Prodigal
[2024-01-24 15:03:30,460] [INFO] Running command: gunzip -c /var/lib/cwl/stge8613960-b859-4afa-ba1a-21c9bf07db39/GCF_010725485.1_ASM1072548v1_genomic.fna.gz | prodigal -d GCF_010725485.1_ASM1072548v1_genomic.fna/cds.fna -a GCF_010725485.1_ASM1072548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:48,960] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:48,960] [INFO] Task started: HMMsearch
[2024-01-24 15:03:48,960] [INFO] Running command: hmmsearch --tblout GCF_010725485.1_ASM1072548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/reference_markers.hmm GCF_010725485.1_ASM1072548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:49,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:49,248] [INFO] Found 6/6 markers.
[2024-01-24 15:03:49,303] [INFO] Query marker FASTA was written to GCF_010725485.1_ASM1072548v1_genomic.fna/markers.fasta
[2024-01-24 15:03:49,303] [INFO] Task started: Blastn
[2024-01-24 15:03:49,303] [INFO] Running command: blastn -query GCF_010725485.1_ASM1072548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/reference_markers.fasta -out GCF_010725485.1_ASM1072548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:50,678] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:50,681] [INFO] Selected 22 target genomes.
[2024-01-24 15:03:50,682] [INFO] Target genome list was writen to GCF_010725485.1_ASM1072548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:50,688] [INFO] Task started: fastANI
[2024-01-24 15:03:50,688] [INFO] Running command: fastANI --query /var/lib/cwl/stge8613960-b859-4afa-ba1a-21c9bf07db39/GCF_010725485.1_ASM1072548v1_genomic.fna.gz --refList GCF_010725485.1_ASM1072548v1_genomic.fna/target_genomes.txt --output GCF_010725485.1_ASM1072548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:18,865] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:18,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:18,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:18,883] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:04:18,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:04:18,883] [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	83.8017	1319	2014	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	83.7045	1460	2014	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	82.6318	1266	2014	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	82.6047	1264	2014	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	82.5788	1246	2014	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	82.4737	1211	2014	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	82.3112	1374	2014	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	82.2747	1379	2014	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.0371	1154	2014	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.0286	1163	2014	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.9718	1169	2014	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	81.1003	1116	2014	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	81.0596	1091	2014	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	80.998	1127	2014	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.3754	1014	2014	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.3277	1018	2014	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.1003	927	2014	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0735	1024	2014	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0563	1027	2014	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8987	932	2014	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.8219	930	2014	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.7267	908	2014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:18,885] [INFO] DFAST Taxonomy check result was written to GCF_010725485.1_ASM1072548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:18,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:18,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:18,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/checkm_data
[2024-01-24 15:04:18,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:18,943] [INFO] Task started: CheckM
[2024-01-24 15:04:18,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010725485.1_ASM1072548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010725485.1_ASM1072548v1_genomic.fna/checkm_input GCF_010725485.1_ASM1072548v1_genomic.fna/checkm_result
[2024-01-24 15:05:28,855] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:28,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:28,875] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:28,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:28,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010725485.1_ASM1072548v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:28,876] [INFO] Task started: Blastn
[2024-01-24 15:05:28,876] [INFO] Running command: blastn -query GCF_010725485.1_ASM1072548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaa81206-0b7f-4364-bb91-371a55f85b54/dqc_reference/reference_markers_gtdb.fasta -out GCF_010725485.1_ASM1072548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:30,968] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:30,972] [INFO] Selected 12 target genomes.
[2024-01-24 15:05:30,972] [INFO] Target genome list was writen to GCF_010725485.1_ASM1072548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:30,979] [INFO] Task started: fastANI
[2024-01-24 15:05:30,979] [INFO] Running command: fastANI --query /var/lib/cwl/stge8613960-b859-4afa-ba1a-21c9bf07db39/GCF_010725485.1_ASM1072548v1_genomic.fna.gz --refList GCF_010725485.1_ASM1072548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010725485.1_ASM1072548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:48,511] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:48,521] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:48,521] [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_010725485.1	s__Mycobacterium sp002946335	100.0	2014	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	conclusive
GCF_002086815.1	s__Mycobacterium parafortuitum	94.7933	1836	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900454025.1	s__Mycobacterium gilvum	84.6669	1447	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_001545925.1	s__Mycobacterium sp001545925	83.8118	1132	2014	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	83.8043	1319	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000612725.1	s__Mycobacterium austroafricanum	83.3973	1360	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_014190915.1	s__Mycobacterium iranicum_B	83.14	1314	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	82.5432	1236	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	82.0126	1163	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_007096635.1	s__Mycobacterium sp007096635	81.6552	1119	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187505.1	s__Mycobacterium goodii_B	80.7093	1086	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637205.1	s__Mycobacterium chitae	80.5653	988	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:48,523] [INFO] GTDB search result was written to GCF_010725485.1_ASM1072548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:48,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:48,530] [INFO] DFAST_QC result json was written to GCF_010725485.1_ASM1072548v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:48,530] [INFO] DFAST_QC completed!
[2024-01-24 15:05:48,530] [INFO] Total running time: 0h2m19s