[2024-01-24 13:40:34,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference
[2024-01-24 13:40:36,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,385] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,386] [INFO] Running command: gunzip -c /var/lib/cwl/stgec029794-a210-4fd7-8f4e-78fa56534b59/GCF_901482605.1_45532_E01_genomic.fna.gz | prodigal -d GCF_901482605.1_45532_E01_genomic.fna/cds.fna -a GCF_901482605.1_45532_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:40,663] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:40,663] [INFO] Task started: HMMsearch
[2024-01-24 13:40:40,663] [INFO] Running command: hmmsearch --tblout GCF_901482605.1_45532_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/reference_markers.hmm GCF_901482605.1_45532_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:40,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:40,945] [INFO] Found 6/6 markers.
[2024-01-24 13:40:40,971] [INFO] Query marker FASTA was written to GCF_901482605.1_45532_E01_genomic.fna/markers.fasta
[2024-01-24 13:40:40,972] [INFO] Task started: Blastn
[2024-01-24 13:40:40,972] [INFO] Running command: blastn -query GCF_901482605.1_45532_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/reference_markers.fasta -out GCF_901482605.1_45532_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:41,663] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:41,667] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:41,667] [INFO] Target genome list was writen to GCF_901482605.1_45532_E01_genomic.fna/target_genomes.txt
[2024-01-24 13:40:41,682] [INFO] Task started: fastANI
[2024-01-24 13:40:41,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgec029794-a210-4fd7-8f4e-78fa56534b59/GCF_901482605.1_45532_E01_genomic.fna.gz --refList GCF_901482605.1_45532_E01_genomic.fna/target_genomes.txt --output GCF_901482605.1_45532_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:51,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:51,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:51,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:51,813] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:51,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:51,814] [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
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	100.0	911	913	95	conclusive
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	80.392	469	913	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	78.4023	73	913	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	78.0363	173	913	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	78.0173	173	913	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.5795	136	913	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.2284	143	913	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	77.0441	157	913	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.9921	123	913	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.8624	119	913	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	76.8288	126	913	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.7231	151	913	95	below_threshold
Clostridium tepidiprofundi	strain=DSM 19306	GCA_001594005.1	420412	420412	type	True	76.6425	118	913	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.2659	134	913	95	below_threshold
Clostridium tyrobutyricum	strain=ATCC 25755	GCA_000359585.1	1519	1519	type	True	76.068	63	913	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000429805.1	1519	1519	type	True	75.9628	64	913	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000392375.2	1519	1519	type	True	75.9347	62	913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:51,815] [INFO] DFAST Taxonomy check result was written to GCF_901482605.1_45532_E01_genomic.fna/tc_result.tsv
[2024-01-24 13:40:51,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:51,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:51,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/checkm_data
[2024-01-24 13:40:51,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:51,851] [INFO] Task started: CheckM
[2024-01-24 13:40:51,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_901482605.1_45532_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_901482605.1_45532_E01_genomic.fna/checkm_input GCF_901482605.1_45532_E01_genomic.fna/checkm_result
[2024-01-24 13:41:13,052] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:13,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,072] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:13,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:13,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_901482605.1_45532_E01_genomic.fna/markers.fasta)
[2024-01-24 13:41:13,073] [INFO] Task started: Blastn
[2024-01-24 13:41:13,073] [INFO] Running command: blastn -query GCF_901482605.1_45532_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6505ef77-aa76-4be2-8da6-d33d8350d622/dqc_reference/reference_markers_gtdb.fasta -out GCF_901482605.1_45532_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:14,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:14,120] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:14,120] [INFO] Target genome list was writen to GCF_901482605.1_45532_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:14,133] [INFO] Task started: fastANI
[2024-01-24 13:41:14,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgec029794-a210-4fd7-8f4e-78fa56534b59/GCF_901482605.1_45532_E01_genomic.fna.gz --refList GCF_901482605.1_45532_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_901482605.1_45532_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:25,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:25,591] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:25,592] [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_901482605.1	s__Hathewaya histolytica	100.0	911	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902143515.1	s__Hathewaya massiliensis	80.3602	468	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003288255.1	s__Hathewaya sp003288255	79.2014	306	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204565.1	s__Clostridium_H botulinum_B	77.9522	136	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.87	99.52	0.98	0.95	19	-
GCF_000816675.1	s__Clostridium_J argentinense	77.7952	171	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCF_014836835.1	s__Clostridium_J sp900547625	77.5395	136	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCA_002341865.1	s__Clostridium_J sp002341865	77.1331	159	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455975.1	s__Clostridium_J sp002455975	77.0611	144	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130005.1	s__Clostridium_D collagenovorans	77.0384	159	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008345.1	s__Clostridium_F tepidum	77.0075	153	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_018918285.1	s__MSJ-11 sp018918285	76.9926	123	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403615.1	s__Desnuesiella massiliensis	76.8083	127	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001594005.1	s__Clostridium_AC tepidiprofundi	76.6809	117	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AC	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205925.1	s__Clostridium_AK peptidivorans	76.6311	114	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129365.1	s__Clostridium_AH fallax	76.2518	135	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000359585.1	s__Clostridium_B tyrobutyricum	76.068	63	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.17	95.02	0.91	0.82	32	-
GCA_002423705.1	s__Clostridium_X sp002423705	75.9681	84	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523855.1	s__UBA3947 sp003541575	75.8211	50	913	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.30	99.30	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,594] [INFO] GTDB search result was written to GCF_901482605.1_45532_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:25,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:25,599] [INFO] DFAST_QC result json was written to GCF_901482605.1_45532_E01_genomic.fna/dqc_result.json
[2024-01-24 13:41:25,599] [INFO] DFAST_QC completed!
[2024-01-24 13:41:25,599] [INFO] Total running time: 0h0m51s