[2023-06-05 05:03:18,159] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:03:18,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:03:18,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference
[2023-06-05 05:03:20,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:03:20,300] [INFO] Task started: Prodigal
[2023-06-05 05:03:20,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg6db8533f-b2e0-40d0-bf50-d587cd72bde4/GCA_934754645.1_ERR7738514_bin.54_genomic.fna.gz | prodigal -d GCA_934754645.1_ERR7738514_bin.54_genomic.fna/cds.fna -a GCA_934754645.1_ERR7738514_bin.54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:03:22,400] [INFO] Task succeeded: Prodigal
[2023-06-05 05:03:22,400] [INFO] Task started: HMMsearch
[2023-06-05 05:03:22,401] [INFO] Running command: hmmsearch --tblout GCA_934754645.1_ERR7738514_bin.54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/reference_markers.hmm GCA_934754645.1_ERR7738514_bin.54_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:03:22,708] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:03:22,709] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6db8533f-b2e0-40d0-bf50-d587cd72bde4/GCA_934754645.1_ERR7738514_bin.54_genomic.fna.gz]
[2023-06-05 05:03:22,731] [INFO] Query marker FASTA was written to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/markers.fasta
[2023-06-05 05:03:22,731] [INFO] Task started: Blastn
[2023-06-05 05:03:22,731] [INFO] Running command: blastn -query GCA_934754645.1_ERR7738514_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/reference_markers.fasta -out GCA_934754645.1_ERR7738514_bin.54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:25,069] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:25,074] [INFO] Selected 18 target genomes.
[2023-06-05 05:03:25,074] [INFO] Target genome list was writen to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/target_genomes.txt
[2023-06-05 05:03:25,075] [INFO] Task started: fastANI
[2023-06-05 05:03:25,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg6db8533f-b2e0-40d0-bf50-d587cd72bde4/GCA_934754645.1_ERR7738514_bin.54_genomic.fna.gz --refList GCA_934754645.1_ERR7738514_bin.54_genomic.fna/target_genomes.txt --output GCA_934754645.1_ERR7738514_bin.54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:03:35,633] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:35,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:03:35,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:03:35,654] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:03:35,654] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:03:35,654] [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
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.07	118	439	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.3706	122	439	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	77.0389	107	439	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.01	114	439	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.9243	115	439	95	below_threshold
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	76.9113	93	439	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	76.9034	98	439	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	76.893	101	439	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	76.8733	121	439	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	76.6545	90	439	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.6327	91	439	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.5175	105	439	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	76.486	96	439	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.4315	88	439	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	76.3158	109	439	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.2662	112	439	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.5588	80	439	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:03:35,657] [INFO] DFAST Taxonomy check result was written to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/tc_result.tsv
[2023-06-05 05:03:35,657] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:03:35,657] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:03:35,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/checkm_data
[2023-06-05 05:03:35,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:03:35,683] [INFO] Task started: CheckM
[2023-06-05 05:03:35,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934754645.1_ERR7738514_bin.54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934754645.1_ERR7738514_bin.54_genomic.fna/checkm_input GCA_934754645.1_ERR7738514_bin.54_genomic.fna/checkm_result
[2023-06-05 05:03:50,312] [INFO] Task succeeded: CheckM
[2023-06-05 05:03:50,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:03:50,336] [INFO] ===== Completeness check finished =====
[2023-06-05 05:03:50,337] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:03:50,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934754645.1_ERR7738514_bin.54_genomic.fna/markers.fasta)
[2023-06-05 05:03:50,338] [INFO] Task started: Blastn
[2023-06-05 05:03:50,338] [INFO] Running command: blastn -query GCA_934754645.1_ERR7738514_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stgc634937c-4e37-4443-a075-bf42ae3e2b0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934754645.1_ERR7738514_bin.54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:51,090] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:51,095] [INFO] Selected 11 target genomes.
[2023-06-05 05:03:51,095] [INFO] Target genome list was writen to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:03:51,098] [INFO] Task started: fastANI
[2023-06-05 05:03:51,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg6db8533f-b2e0-40d0-bf50-d587cd72bde4/GCA_934754645.1_ERR7738514_bin.54_genomic.fna.gz --refList GCA_934754645.1_ERR7738514_bin.54_genomic.fna/target_genomes_gtdb.txt --output GCA_934754645.1_ERR7738514_bin.54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:03:57,111] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:57,128] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:03:57,128] [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_900539375.1	s__Clostridium sp900539375	98.975	391	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	conclusive
GCA_900317445.1	s__Clostridium sp900317445	92.8944	283	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902785295.1	s__Clostridium sp902785295	88.9578	339	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519155.1	s__Clostridium sp012519155	78.3618	112	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900447045.1	s__Clostridium paraputrificum	78.07	118	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCA_018372875.1	s__Clostridium sp018372875	77.9066	111	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCA_015058405.1	s__Clostridium sp015058405	77.5816	124	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519845.1	s__Clostridium sp012519845	77.4209	130	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116755.1	s__Clostridium sp900116755	77.403	125	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058375.1	s__Clostridium sp015058375	77.1634	103	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	77.146	110	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
--------------------------------------------------------------------------------
[2023-06-05 05:03:57,130] [INFO] GTDB search result was written to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/result_gtdb.tsv
[2023-06-05 05:03:57,131] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:03:57,134] [INFO] DFAST_QC result json was written to GCA_934754645.1_ERR7738514_bin.54_genomic.fna/dqc_result.json
[2023-06-05 05:03:57,135] [INFO] DFAST_QC completed!
[2023-06-05 05:03:57,135] [INFO] Total running time: 0h0m39s