[2023-06-04 17:35:16,718] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:35:16,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:35:16,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference
[2023-06-04 17:35:19,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:35:19,271] [INFO] Task started: Prodigal
[2023-06-04 17:35:19,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fbd5ae2-e2af-4cf6-a7d4-1ff40453d898/GCA_934630935.1_ERR7738937_bin.117_genomic.fna.gz | prodigal -d GCA_934630935.1_ERR7738937_bin.117_genomic.fna/cds.fna -a GCA_934630935.1_ERR7738937_bin.117_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:35:25,945] [INFO] Task succeeded: Prodigal
[2023-06-04 17:35:25,946] [INFO] Task started: HMMsearch
[2023-06-04 17:35:25,946] [INFO] Running command: hmmsearch --tblout GCA_934630935.1_ERR7738937_bin.117_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/reference_markers.hmm GCA_934630935.1_ERR7738937_bin.117_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:35:26,182] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:35:26,184] [INFO] Found 6/6 markers.
[2023-06-04 17:35:26,210] [INFO] Query marker FASTA was written to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/markers.fasta
[2023-06-04 17:35:26,211] [INFO] Task started: Blastn
[2023-06-04 17:35:26,211] [INFO] Running command: blastn -query GCA_934630935.1_ERR7738937_bin.117_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/reference_markers.fasta -out GCA_934630935.1_ERR7738937_bin.117_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:26,901] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:26,906] [INFO] Selected 13 target genomes.
[2023-06-04 17:35:26,907] [INFO] Target genome list was writen to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/target_genomes.txt
[2023-06-04 17:35:26,915] [INFO] Task started: fastANI
[2023-06-04 17:35:26,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fbd5ae2-e2af-4cf6-a7d4-1ff40453d898/GCA_934630935.1_ERR7738937_bin.117_genomic.fna.gz --refList GCA_934630935.1_ERR7738937_bin.117_genomic.fna/target_genomes.txt --output GCA_934630935.1_ERR7738937_bin.117_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:35:33,784] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:33,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:35:33,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:35:33,801] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 17:35:33,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 17:35:33,801] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	99.5342	719	737	95	conclusive
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.562	285	737	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.0046	270	737	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.493	204	737	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.4836	191	737	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.4699	210	737	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.3612	159	737	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.3575	235	737	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.3508	204	737	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.0776	194	737	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.557	65	737	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	76.532	67	737	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:35:33,803] [INFO] DFAST Taxonomy check result was written to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/tc_result.tsv
[2023-06-04 17:35:33,804] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:35:33,804] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:35:33,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/checkm_data
[2023-06-04 17:35:33,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:35:33,832] [INFO] Task started: CheckM
[2023-06-04 17:35:33,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630935.1_ERR7738937_bin.117_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630935.1_ERR7738937_bin.117_genomic.fna/checkm_input GCA_934630935.1_ERR7738937_bin.117_genomic.fna/checkm_result
[2023-06-04 17:35:58,833] [INFO] Task succeeded: CheckM
[2023-06-04 17:35:58,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:35:58,855] [INFO] ===== Completeness check finished =====
[2023-06-04 17:35:58,855] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:35:58,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630935.1_ERR7738937_bin.117_genomic.fna/markers.fasta)
[2023-06-04 17:35:58,856] [INFO] Task started: Blastn
[2023-06-04 17:35:58,856] [INFO] Running command: blastn -query GCA_934630935.1_ERR7738937_bin.117_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7903c52-c38f-4252-a552-9d1d53778c9e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630935.1_ERR7738937_bin.117_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:36:00,154] [INFO] Task succeeded: Blastn
[2023-06-04 17:36:00,159] [INFO] Selected 8 target genomes.
[2023-06-04 17:36:00,159] [INFO] Target genome list was writen to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:36:00,250] [INFO] Task started: fastANI
[2023-06-04 17:36:00,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fbd5ae2-e2af-4cf6-a7d4-1ff40453d898/GCA_934630935.1_ERR7738937_bin.117_genomic.fna.gz --refList GCA_934630935.1_ERR7738937_bin.117_genomic.fna/target_genomes_gtdb.txt --output GCA_934630935.1_ERR7738937_bin.117_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:36:05,053] [INFO] Task succeeded: fastANI
[2023-06-04 17:36:05,067] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:36:05,067] [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_005121165.2	s__Dysosmobacter welbionis	99.5342	719	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	conclusive
GCA_019118935.1	s__Dysosmobacter pullicola	94.1914	602	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019118505.1	s__Dysosmobacter excrementavium	88.6246	513	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	88.6001	551	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	88.3983	578	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCF_018228705.1	s__Dysosmobacter sp018228705	83.7434	495	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	82.5181	421	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:36:05,069] [INFO] GTDB search result was written to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/result_gtdb.tsv
[2023-06-04 17:36:05,070] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:36:05,075] [INFO] DFAST_QC result json was written to GCA_934630935.1_ERR7738937_bin.117_genomic.fna/dqc_result.json
[2023-06-04 17:36:05,075] [INFO] DFAST_QC completed!
[2023-06-04 17:36:05,076] [INFO] Total running time: 0h0m48s