[2024-01-24 13:24:48,158] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,160] [INFO] DQC Reference Directory: /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference
[2024-01-24 13:24:49,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,527] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,527] [INFO] Running command: gunzip -c /var/lib/cwl/stge4deb4c4-6b2e-44f3-adbd-281b17f03112/GCF_003363435.1_ASM336343v1_genomic.fna.gz | prodigal -d GCF_003363435.1_ASM336343v1_genomic.fna/cds.fna -a GCF_003363435.1_ASM336343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:57,000] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:57,001] [INFO] Task started: HMMsearch
[2024-01-24 13:24:57,001] [INFO] Running command: hmmsearch --tblout GCF_003363435.1_ASM336343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/reference_markers.hmm GCF_003363435.1_ASM336343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:57,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:57,303] [INFO] Found 6/6 markers.
[2024-01-24 13:24:57,342] [INFO] Query marker FASTA was written to GCF_003363435.1_ASM336343v1_genomic.fna/markers.fasta
[2024-01-24 13:24:57,342] [INFO] Task started: Blastn
[2024-01-24 13:24:57,342] [INFO] Running command: blastn -query GCF_003363435.1_ASM336343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/reference_markers.fasta -out GCF_003363435.1_ASM336343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:58,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:58,073] [INFO] Selected 24 target genomes.
[2024-01-24 13:24:58,073] [INFO] Target genome list was writen to GCF_003363435.1_ASM336343v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:58,102] [INFO] Task started: fastANI
[2024-01-24 13:24:58,102] [INFO] Running command: fastANI --query /var/lib/cwl/stge4deb4c4-6b2e-44f3-adbd-281b17f03112/GCF_003363435.1_ASM336343v1_genomic.fna.gz --refList GCF_003363435.1_ASM336343v1_genomic.fna/target_genomes.txt --output GCF_003363435.1_ASM336343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:14,009] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:14,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:14,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:14,024] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:14,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:14,024] [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
Anaerosacchariphilus polymeriproducens	strain=MCWD5	GCA_003363435.1	1812858	1812858	type	True	100.0	1245	1245	95	conclusive
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	77.0402	71	1245	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	76.9731	76	1245	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.9502	102	1245	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	76.6951	63	1245	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	76.6544	53	1245	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	76.6204	63	1245	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	76.3675	67	1245	95	below_threshold
[Clostridium] populeti	strain=743A	GCA_900112775.1	37658	37658	type	True	76.2113	67	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:14,026] [INFO] DFAST Taxonomy check result was written to GCF_003363435.1_ASM336343v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:14,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:14,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:14,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/checkm_data
[2024-01-24 13:25:14,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:14,068] [INFO] Task started: CheckM
[2024-01-24 13:25:14,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363435.1_ASM336343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363435.1_ASM336343v1_genomic.fna/checkm_input GCF_003363435.1_ASM336343v1_genomic.fna/checkm_result
[2024-01-24 13:25:41,676] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:41,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:41,702] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:41,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:41,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363435.1_ASM336343v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:41,704] [INFO] Task started: Blastn
[2024-01-24 13:25:41,704] [INFO] Running command: blastn -query GCF_003363435.1_ASM336343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga141738c-c04c-43a0-8ec4-e449dd4c9228/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363435.1_ASM336343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:42,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:42,700] [INFO] Selected 28 target genomes.
[2024-01-24 13:25:42,700] [INFO] Target genome list was writen to GCF_003363435.1_ASM336343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:42,784] [INFO] Task started: fastANI
[2024-01-24 13:25:42,784] [INFO] Running command: fastANI --query /var/lib/cwl/stge4deb4c4-6b2e-44f3-adbd-281b17f03112/GCF_003363435.1_ASM336343v1_genomic.fna.gz --refList GCF_003363435.1_ASM336343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363435.1_ASM336343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:57,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:57,606] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:57,607] [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_003363435.1	s__Anaerosacchariphilus polymeriproducens	100.0	1245	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosacchariphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008830185.1	s__Lachnotalea soehngenii	77.4712	111	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	98.91	98.91	0.90	0.90	2	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	76.9731	76	1245	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_003201285.1	s__Lachnotalea glycerini	76.9719	101	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	99.47	99.47	0.92	0.92	2	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.8229	62	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_910575005.1	s__14-2 sp910575005	76.6749	56	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.96	99.90	0.99	0.99	4	-
GCA_000403255.2	s__14-2 sp000403255	76.6153	53	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	99.01	0.96	0.96	2	-
GCA_017436305.1	s__RGIG3040 sp017436305	76.4698	51	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540475.1	s__Robinsoniella sp900540475	76.3694	58	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.99	99.99	0.98	0.98	2	-
GCA_012519695.1	s__14-2 sp012519695	76.3108	79	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	97.81	97.81	0.86	0.86	2	-
GCF_900111325.1	s__Lachnobacterium bovis_A	76.2869	62	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnobacterium	95.0	99.27	99.17	0.94	0.94	4	-
GCA_017416465.1	s__CAG-603 sp017416465	76.2772	63	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	76.2337	62	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_910585935.1	s__MGBC136627 sp910585935	76.1635	63	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MGBC136627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399445.1	s__RUG11237 sp017399445	76.1497	79	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11237	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003481745.1	s__Blautia stercoris	76.143	63	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCA_905215405.1	s__Clostridium_N sp905215405	76.0768	51	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544525.1	s__Scybalomonas sp900544525	75.9904	54	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scybalomonas	95.0	98.74	97.44	0.82	0.73	4	-
GCA_910586005.1	s__14-2 sp910586005	75.8987	86	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547685.1	s__Blautia sp900547685	75.8772	54	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201915.1	s__Blautia sp900555025	75.7608	51	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
GCA_017625255.1	s__1XD42-69 sp017625255	75.7417	56	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576895.1	s__MGBC100174 sp910576895	75.5336	68	1245	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MGBC100174	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:57,609] [INFO] GTDB search result was written to GCF_003363435.1_ASM336343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:57,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:57,613] [INFO] DFAST_QC result json was written to GCF_003363435.1_ASM336343v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:57,613] [INFO] DFAST_QC completed!
[2024-01-24 13:25:57,613] [INFO] Total running time: 0h1m9s