[2024-01-24 12:57:50,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference
[2024-01-24 12:57:51,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,541] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b6ff894-aaef-4cc5-b62f-e83266d3a849/GCF_009696045.1_ASM969604v1_genomic.fna.gz | prodigal -d GCF_009696045.1_ASM969604v1_genomic.fna/cds.fna -a GCF_009696045.1_ASM969604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:57:57,509] [INFO] Task succeeded: Prodigal
[2024-01-24 12:57:57,510] [INFO] Task started: HMMsearch
[2024-01-24 12:57:57,510] [INFO] Running command: hmmsearch --tblout GCF_009696045.1_ASM969604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/reference_markers.hmm GCF_009696045.1_ASM969604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:57:57,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:57:57,721] [INFO] Found 6/6 markers.
[2024-01-24 12:57:57,746] [INFO] Query marker FASTA was written to GCF_009696045.1_ASM969604v1_genomic.fna/markers.fasta
[2024-01-24 12:57:57,746] [INFO] Task started: Blastn
[2024-01-24 12:57:57,746] [INFO] Running command: blastn -query GCF_009696045.1_ASM969604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/reference_markers.fasta -out GCF_009696045.1_ASM969604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:57:58,346] [INFO] Task succeeded: Blastn
[2024-01-24 12:57:58,349] [INFO] Selected 24 target genomes.
[2024-01-24 12:57:58,350] [INFO] Target genome list was writen to GCF_009696045.1_ASM969604v1_genomic.fna/target_genomes.txt
[2024-01-24 12:57:58,359] [INFO] Task started: fastANI
[2024-01-24 12:57:58,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6ff894-aaef-4cc5-b62f-e83266d3a849/GCF_009696045.1_ASM969604v1_genomic.fna.gz --refList GCF_009696045.1_ASM969604v1_genomic.fna/target_genomes.txt --output GCF_009696045.1_ASM969604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:12,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:12,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:12,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:12,157] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:12,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:12,157] [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
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	100.0	994	997	95	conclusive
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.9703	60	997	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.5053	93	997	95	below_threshold
[Clostridium] populeti	strain=743A	GCA_900112775.1	37658	37658	type	True	77.3448	91	997	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	77.1984	71	997	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	77.1627	83	997	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.117	83	997	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	77.0344	91	997	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	76.9134	104	997	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	76.8525	69	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:12,159] [INFO] DFAST Taxonomy check result was written to GCF_009696045.1_ASM969604v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:12,160] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:12,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:12,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/checkm_data
[2024-01-24 12:58:12,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:12,191] [INFO] Task started: CheckM
[2024-01-24 12:58:12,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696045.1_ASM969604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696045.1_ASM969604v1_genomic.fna/checkm_input GCF_009696045.1_ASM969604v1_genomic.fna/checkm_result
[2024-01-24 12:58:35,445] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:35,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:35,467] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:35,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:35,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696045.1_ASM969604v1_genomic.fna/markers.fasta)
[2024-01-24 12:58:35,468] [INFO] Task started: Blastn
[2024-01-24 12:58:35,468] [INFO] Running command: blastn -query GCF_009696045.1_ASM969604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78bc567d-fda8-4f94-bb29-a7b7e1accf03/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696045.1_ASM969604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:36,462] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:36,466] [INFO] Selected 21 target genomes.
[2024-01-24 12:58:36,466] [INFO] Target genome list was writen to GCF_009696045.1_ASM969604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:36,483] [INFO] Task started: fastANI
[2024-01-24 12:58:36,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6ff894-aaef-4cc5-b62f-e83266d3a849/GCF_009696045.1_ASM969604v1_genomic.fna.gz --refList GCF_009696045.1_ASM969604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696045.1_ASM969604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:58:49,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:49,295] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:58:49,296] [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_009696045.1	s__Velocimicrobium porci	100.0	994	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001461035.1	s__Velocimicrobium ethanolgignens	78.7275	111	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009731425.1	s__KM106-2 sp009731425	77.8646	97	997	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_002419585.1	s__Velocimicrobium sp002419585	77.7806	122	997	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_018883985.1	s__Ruminococcus_B intestinipullorum	77.6229	51	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003481745.1	s__Blautia stercoris	77.2464	76	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCF_000018685.1	s__Lachnoclostridium phytofermentans	77.1984	71	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111595.1	s__Clostridium_AI polysaccharolyticum	77.1627	83	997	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_017399885.1	s__CAG-411 sp017399885	77.1365	62	997	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	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	77.117	83	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	77.0344	91	997	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_000702945.1	s__Anaerocolumna sp000702945	77.0179	59	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078195.1	s__Lachnoclostridium sp900078195	76.9597	100	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142955.1	s__Anaerosporobacter mobilis	76.9134	104	997	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_003526525.1	s__Lachnoclostridium sp003526525	76.8729	54	997	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	76.8692	82	997	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	-
GCF_014218355.1	s__Anaerocolumna sp014218355	76.8578	68	997	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_002297865.1	s__Clostridium_AI sp002297865	76.8322	88	997	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_015057635.1	s__Lachnoclostridium sp015057635	76.7264	58	997	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_017393285.1	s__CAG-411 sp017393285	76.5635	53	997	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:58:49,297] [INFO] GTDB search result was written to GCF_009696045.1_ASM969604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:58:49,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:58:49,303] [INFO] DFAST_QC result json was written to GCF_009696045.1_ASM969604v1_genomic.fna/dqc_result.json
[2024-01-24 12:58:49,303] [INFO] DFAST_QC completed!
[2024-01-24 12:58:49,303] [INFO] Total running time: 0h0m59s