[2024-01-24 10:58:18,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:18,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:18,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference
[2024-01-24 10:58:19,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:19,216] [INFO] Task started: Prodigal
[2024-01-24 10:58:19,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg006cda76-ade9-4d0e-9d13-4a05b53778df/GCF_016591975.1_ASM1659197v1_genomic.fna.gz | prodigal -d GCF_016591975.1_ASM1659197v1_genomic.fna/cds.fna -a GCF_016591975.1_ASM1659197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:28,369] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:28,370] [INFO] Task started: HMMsearch
[2024-01-24 10:58:28,370] [INFO] Running command: hmmsearch --tblout GCF_016591975.1_ASM1659197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/reference_markers.hmm GCF_016591975.1_ASM1659197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:28,664] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:28,666] [INFO] Found 6/6 markers.
[2024-01-24 10:58:28,709] [INFO] Query marker FASTA was written to GCF_016591975.1_ASM1659197v1_genomic.fna/markers.fasta
[2024-01-24 10:58:28,710] [INFO] Task started: Blastn
[2024-01-24 10:58:28,710] [INFO] Running command: blastn -query GCF_016591975.1_ASM1659197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/reference_markers.fasta -out GCF_016591975.1_ASM1659197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:29,350] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:29,355] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:29,355] [INFO] Target genome list was writen to GCF_016591975.1_ASM1659197v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:29,379] [INFO] Task started: fastANI
[2024-01-24 10:58:29,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg006cda76-ade9-4d0e-9d13-4a05b53778df/GCF_016591975.1_ASM1659197v1_genomic.fna.gz --refList GCF_016591975.1_ASM1659197v1_genomic.fna/target_genomes.txt --output GCF_016591975.1_ASM1659197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:42,782] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:42,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:42,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:42,798] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:42,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:42,798] [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
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	78.6548	108	1696	95	below_threshold
Anaerocolumna cellulosilytica	strain=SN021	GCA_014218335.1	433286	433286	type	True	78.611	115	1696	95	below_threshold
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	78.3981	115	1696	95	below_threshold
Vallitalea pronyensis	strain=FatNI3	GCA_018141445.1	1348613	1348613	type	True	78.2652	51	1696	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	77.9443	158	1696	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.8881	168	1696	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	77.7249	182	1696	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.5785	107	1696	95	below_threshold
Mobilitalea sibirica	strain=DSM 26468	GCA_015999265.1	1462919	1462919	type	True	77.2951	63	1696	95	below_threshold
Anaerocolumna cellulosilytica	strain=DSM 100423	GCA_014202875.1	433286	433286	type	True	77.0285	110	1696	95	below_threshold
Anaerosacchariphilus polymeriproducens	strain=MCWD5	GCA_003363435.1	1812858	1812858	type	True	76.9545	73	1696	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.5189	86	1696	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	76.2666	94	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:42,800] [INFO] DFAST Taxonomy check result was written to GCF_016591975.1_ASM1659197v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:42,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:42,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:42,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/checkm_data
[2024-01-24 10:58:42,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:42,859] [INFO] Task started: CheckM
[2024-01-24 10:58:42,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016591975.1_ASM1659197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016591975.1_ASM1659197v1_genomic.fna/checkm_input GCF_016591975.1_ASM1659197v1_genomic.fna/checkm_result
[2024-01-24 10:59:16,311] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:16,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:16,335] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:16,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:16,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016591975.1_ASM1659197v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:16,336] [INFO] Task started: Blastn
[2024-01-24 10:59:16,336] [INFO] Running command: blastn -query GCF_016591975.1_ASM1659197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff4164ed-013a-4b3a-8c7c-27062a4e8346/dqc_reference/reference_markers_gtdb.fasta -out GCF_016591975.1_ASM1659197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:17,345] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:17,350] [INFO] Selected 19 target genomes.
[2024-01-24 10:59:17,350] [INFO] Target genome list was writen to GCF_016591975.1_ASM1659197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:17,373] [INFO] Task started: fastANI
[2024-01-24 10:59:17,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg006cda76-ade9-4d0e-9d13-4a05b53778df/GCF_016591975.1_ASM1659197v1_genomic.fna.gz --refList GCF_016591975.1_ASM1659197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016591975.1_ASM1659197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:30,367] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:30,386] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:30,386] [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
GCA_016591975.1	s__TB5 sp016591975	100.0	1693	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009731425.1	s__KM106-2 sp009731425	78.4005	155	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018372435.1	s__Anaerosporobacter sp018372435	78.0109	161	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	96.90	96.04	0.88	0.87	3	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	77.9646	157	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	77.8881	168	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142955.1	s__Anaerosporobacter mobilis	77.7267	180	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078195.1	s__Lachnoclostridium sp900078195	77.6699	139	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905214875.1	s__KM106-2 sp905214875	77.651	107	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390525.1	s__RGIG989 sp017390525	77.6364	61	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG989	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	77.5462	107	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCA_002294045.1	s__Anaerocolumna sp002294045	77.0839	58	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419585.1	s__Velocimicrobium sp002419585	77.0772	94	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297865.1	s__Clostridium_AI sp002297865	76.876	77	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201285.1	s__Lachnotalea glycerini	76.5399	84	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	99.47	99.47	0.92	0.92	2	-
GCA_905192625.1	s__Lachnoclostridium sp905192625	76.534	52	1696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:30,387] [INFO] GTDB search result was written to GCF_016591975.1_ASM1659197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:30,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:30,392] [INFO] DFAST_QC result json was written to GCF_016591975.1_ASM1659197v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:30,392] [INFO] DFAST_QC completed!
[2024-01-24 10:59:30,392] [INFO] Total running time: 0h1m12s