[2024-01-24 15:18:05,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference
[2024-01-24 15:18:07,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,531] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf1e8e11-8768-456d-9528-d474c80f31b6/GCF_012070565.1_ASM1207056v1_genomic.fna.gz | prodigal -d GCF_012070565.1_ASM1207056v1_genomic.fna/cds.fna -a GCF_012070565.1_ASM1207056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:17,565] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:17,565] [INFO] Task started: HMMsearch
[2024-01-24 15:18:17,566] [INFO] Running command: hmmsearch --tblout GCF_012070565.1_ASM1207056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/reference_markers.hmm GCF_012070565.1_ASM1207056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:17,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:17,924] [INFO] Found 6/6 markers.
[2024-01-24 15:18:17,970] [INFO] Query marker FASTA was written to GCF_012070565.1_ASM1207056v1_genomic.fna/markers.fasta
[2024-01-24 15:18:17,970] [INFO] Task started: Blastn
[2024-01-24 15:18:17,970] [INFO] Running command: blastn -query GCF_012070565.1_ASM1207056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/reference_markers.fasta -out GCF_012070565.1_ASM1207056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:18,636] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:18,640] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:18,641] [INFO] Target genome list was writen to GCF_012070565.1_ASM1207056v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:18,769] [INFO] Task started: fastANI
[2024-01-24 15:18:18,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf1e8e11-8768-456d-9528-d474c80f31b6/GCF_012070565.1_ASM1207056v1_genomic.fna.gz --refList GCF_012070565.1_ASM1207056v1_genomic.fna/target_genomes.txt --output GCF_012070565.1_ASM1207056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:33,045] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:33,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:33,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:33,059] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:33,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:33,059] [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
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	100.0	1499	1503	95	conclusive
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	79.8121	489	1503	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.9528	98	1503	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	77.2947	85	1503	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	77.2564	86	1503	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	77.1575	82	1503	95	below_threshold
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	77.1384	97	1503	95	below_threshold
Anaerosacchariphilus polymeriproducens	strain=MCWD5	GCA_003363435.1	1812858	1812858	type	True	76.7588	59	1503	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	76.657	52	1503	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	76.5839	64	1503	95	below_threshold
[Clostridium] populeti	strain=743A	GCA_900112775.1	37658	37658	type	True	76.4701	84	1503	95	below_threshold
Mobilitalea sibirica	strain=DSM 26468	GCA_015999265.1	1462919	1462919	type	True	75.9969	55	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:33,065] [INFO] DFAST Taxonomy check result was written to GCF_012070565.1_ASM1207056v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:33,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:33,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:33,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/checkm_data
[2024-01-24 15:18:33,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:33,112] [INFO] Task started: CheckM
[2024-01-24 15:18:33,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012070565.1_ASM1207056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012070565.1_ASM1207056v1_genomic.fna/checkm_input GCF_012070565.1_ASM1207056v1_genomic.fna/checkm_result
[2024-01-24 15:19:08,768] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:08,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:08,791] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:08,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:08,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012070565.1_ASM1207056v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:08,792] [INFO] Task started: Blastn
[2024-01-24 15:19:08,792] [INFO] Running command: blastn -query GCF_012070565.1_ASM1207056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5032ce4e-1431-409c-ba57-72f2656db4ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_012070565.1_ASM1207056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:09,840] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:09,844] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:09,844] [INFO] Target genome list was writen to GCF_012070565.1_ASM1207056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:09,862] [INFO] Task started: fastANI
[2024-01-24 15:19:09,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf1e8e11-8768-456d-9528-d474c80f31b6/GCF_012070565.1_ASM1207056v1_genomic.fna.gz --refList GCF_012070565.1_ASM1207056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012070565.1_ASM1207056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:19,802] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:19,816] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:19,816] [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_012070565.1	s__Anaerosporobacter sp012070565	100.0	1498	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018372435.1	s__Anaerosporobacter sp018372435	79.8741	456	1503	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_900142955.1	s__Anaerosporobacter mobilis	79.8049	491	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	77.8792	155	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009731425.1	s__KM106-2 sp009731425	77.5581	134	1503	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_905214875.1	s__KM106-2 sp905214875	77.5291	117	1503	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	-
GCF_900078195.1	s__Lachnoclostridium sp900078195	77.0948	114	1503	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_002297865.1	s__Clostridium_AI sp002297865	77.0301	87	1503	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	-
GCA_014799595.1	s__CAG-411 sp014799595	76.9828	59	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526525.1	s__Lachnoclostridium sp003526525	76.9087	76	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437275.1	s__CAG-411 sp000437275	76.6302	76	1503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-411	95.0	99.92	99.91	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:19,818] [INFO] GTDB search result was written to GCF_012070565.1_ASM1207056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:19,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:19,822] [INFO] DFAST_QC result json was written to GCF_012070565.1_ASM1207056v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:19,822] [INFO] DFAST_QC completed!
[2024-01-24 15:19:19,822] [INFO] Total running time: 0h1m15s