[2023-06-05 10:12:27,404] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:12:27,407] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:12:27,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference
[2023-06-05 10:12:29,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:12:29,659] [INFO] Task started: Prodigal
[2023-06-05 10:12:29,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ba6379d-a62f-4c9c-8a01-cd302914eb38/GCA_934567495.1_ERR7745719_bin.111_genomic.fna.gz | prodigal -d GCA_934567495.1_ERR7745719_bin.111_genomic.fna/cds.fna -a GCA_934567495.1_ERR7745719_bin.111_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:12:33,488] [INFO] Task succeeded: Prodigal
[2023-06-05 10:12:33,489] [INFO] Task started: HMMsearch
[2023-06-05 10:12:33,489] [INFO] Running command: hmmsearch --tblout GCA_934567495.1_ERR7745719_bin.111_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/reference_markers.hmm GCA_934567495.1_ERR7745719_bin.111_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:12:33,747] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:12:33,748] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4ba6379d-a62f-4c9c-8a01-cd302914eb38/GCA_934567495.1_ERR7745719_bin.111_genomic.fna.gz]
[2023-06-05 10:12:33,874] [INFO] Query marker FASTA was written to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/markers.fasta
[2023-06-05 10:12:33,874] [INFO] Task started: Blastn
[2023-06-05 10:12:33,874] [INFO] Running command: blastn -query GCA_934567495.1_ERR7745719_bin.111_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/reference_markers.fasta -out GCA_934567495.1_ERR7745719_bin.111_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:12:34,484] [INFO] Task succeeded: Blastn
[2023-06-05 10:12:34,490] [INFO] Selected 24 target genomes.
[2023-06-05 10:12:34,491] [INFO] Target genome list was writen to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/target_genomes.txt
[2023-06-05 10:12:34,523] [INFO] Task started: fastANI
[2023-06-05 10:12:34,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba6379d-a62f-4c9c-8a01-cd302914eb38/GCA_934567495.1_ERR7745719_bin.111_genomic.fna.gz --refList GCA_934567495.1_ERR7745719_bin.111_genomic.fna/target_genomes.txt --output GCA_934567495.1_ERR7745719_bin.111_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:12:51,417] [INFO] Task succeeded: fastANI
[2023-06-05 10:12:51,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:12:51,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:12:51,430] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:12:51,430] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:12:51,430] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.6141	128	428	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.5467	106	428	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9311	106	428	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.8585	62	428	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7953	113	428	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.5045	78	428	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.3832	79	428	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.3284	89	428	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.252	88	428	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.1122	67	428	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.7309	50	428	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.3198	70	428	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:12:51,434] [INFO] DFAST Taxonomy check result was written to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/tc_result.tsv
[2023-06-05 10:12:51,435] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:12:51,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:12:51,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/checkm_data
[2023-06-05 10:12:51,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:12:51,523] [INFO] Task started: CheckM
[2023-06-05 10:12:51,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934567495.1_ERR7745719_bin.111_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934567495.1_ERR7745719_bin.111_genomic.fna/checkm_input GCA_934567495.1_ERR7745719_bin.111_genomic.fna/checkm_result
[2023-06-05 10:13:11,805] [INFO] Task succeeded: CheckM
[2023-06-05 10:13:11,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:13:11,826] [INFO] ===== Completeness check finished =====
[2023-06-05 10:13:11,827] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:13:11,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934567495.1_ERR7745719_bin.111_genomic.fna/markers.fasta)
[2023-06-05 10:13:11,828] [INFO] Task started: Blastn
[2023-06-05 10:13:11,828] [INFO] Running command: blastn -query GCA_934567495.1_ERR7745719_bin.111_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d4ddab0-cb43-472f-a620-72e411242224/dqc_reference/reference_markers_gtdb.fasta -out GCA_934567495.1_ERR7745719_bin.111_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:13:12,836] [INFO] Task succeeded: Blastn
[2023-06-05 10:13:12,841] [INFO] Selected 14 target genomes.
[2023-06-05 10:13:12,841] [INFO] Target genome list was writen to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:13:12,849] [INFO] Task started: fastANI
[2023-06-05 10:13:12,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba6379d-a62f-4c9c-8a01-cd302914eb38/GCA_934567495.1_ERR7745719_bin.111_genomic.fna.gz --refList GCA_934567495.1_ERR7745719_bin.111_genomic.fna/target_genomes_gtdb.txt --output GCA_934567495.1_ERR7745719_bin.111_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:13:17,864] [INFO] Task succeeded: fastANI
[2023-06-05 10:13:17,881] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-05 10:13:17,881] [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_018918025.1	s__ER4 sp900317525	98.4257	415	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.58	97.23	0.91	0.84	22	inconclusive
GCA_002437735.1	s__ER4 sp002437735	95.4319	311	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.63	99.63	0.85	0.85	2	inconclusive
GCA_900552375.1	s__ER4 sp900552375	88.3471	332	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002405995.1	s__ER4 sp002405995	82.1695	264	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900546295.1	s__ER4 sp900546295	82.0312	270	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCF_000765235.1	s__ER4 sp000765235	81.806	277	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	-
GCA_900552015.1	s__ER4 sp900552015	81.7499	250	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900556145.1	s__ER4 sp900556145	81.6761	180	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550165.1	s__ER4 sp900550165	81.6062	260	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_900768135.1	s__ER4 sp900768135	81.5553	243	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295615.1	s__ER4 sp016295615	80.6619	179	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.52	97.90	0.85	0.84	3	-
GCA_900552475.1	s__CAG-83 sp900552475	79.2546	171	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.74	98.42	0.88	0.85	4	-
GCA_902388735.1	s__CAG-83 sp902388735	78.566	116	428	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:13:17,884] [INFO] GTDB search result was written to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/result_gtdb.tsv
[2023-06-05 10:13:17,884] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:13:17,888] [INFO] DFAST_QC result json was written to GCA_934567495.1_ERR7745719_bin.111_genomic.fna/dqc_result.json
[2023-06-05 10:13:17,888] [INFO] DFAST_QC completed!
[2023-06-05 10:13:17,888] [INFO] Total running time: 0h0m50s