[2023-06-04 23:48:10,787] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:48:10,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:48:10,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference
[2023-06-04 23:48:12,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:48:12,725] [INFO] Task started: Prodigal
[2023-06-04 23:48:12,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg76ebfea2-8c56-43ca-8c8a-65b97f5ae1b5/GCA_934574045.1_ERR7746217_bin.293_genomic.fna.gz | prodigal -d GCA_934574045.1_ERR7746217_bin.293_genomic.fna/cds.fna -a GCA_934574045.1_ERR7746217_bin.293_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:48:18,778] [INFO] Task succeeded: Prodigal
[2023-06-04 23:48:18,778] [INFO] Task started: HMMsearch
[2023-06-04 23:48:18,778] [INFO] Running command: hmmsearch --tblout GCA_934574045.1_ERR7746217_bin.293_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/reference_markers.hmm GCA_934574045.1_ERR7746217_bin.293_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:48:19,037] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:48:19,038] [INFO] Found 6/6 markers.
[2023-06-04 23:48:19,065] [INFO] Query marker FASTA was written to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/markers.fasta
[2023-06-04 23:48:19,066] [INFO] Task started: Blastn
[2023-06-04 23:48:19,066] [INFO] Running command: blastn -query GCA_934574045.1_ERR7746217_bin.293_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/reference_markers.fasta -out GCA_934574045.1_ERR7746217_bin.293_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:19,815] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:19,819] [INFO] Selected 12 target genomes.
[2023-06-04 23:48:19,819] [INFO] Target genome list was writen to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/target_genomes.txt
[2023-06-04 23:48:19,820] [INFO] Task started: fastANI
[2023-06-04 23:48:19,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ebfea2-8c56-43ca-8c8a-65b97f5ae1b5/GCA_934574045.1_ERR7746217_bin.293_genomic.fna.gz --refList GCA_934574045.1_ERR7746217_bin.293_genomic.fna/target_genomes.txt --output GCA_934574045.1_ERR7746217_bin.293_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:48:25,890] [INFO] Task succeeded: fastANI
[2023-06-04 23:48:25,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:48:25,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:48:25,901] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:48:25,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:48:25,901] [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
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	81.5593	443	717	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.9854	362	717	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.9046	268	717	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.5973	191	717	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.3205	226	717	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.9869	147	717	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.8651	172	717	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.7102	165	717	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.5315	182	717	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.0103	124	717	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.75	88	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:48:25,903] [INFO] DFAST Taxonomy check result was written to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/tc_result.tsv
[2023-06-04 23:48:25,904] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:48:25,904] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:48:25,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/checkm_data
[2023-06-04 23:48:25,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:48:25,930] [INFO] Task started: CheckM
[2023-06-04 23:48:25,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934574045.1_ERR7746217_bin.293_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934574045.1_ERR7746217_bin.293_genomic.fna/checkm_input GCA_934574045.1_ERR7746217_bin.293_genomic.fna/checkm_result
[2023-06-04 23:48:49,856] [INFO] Task succeeded: CheckM
[2023-06-04 23:48:49,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:48:49,877] [INFO] ===== Completeness check finished =====
[2023-06-04 23:48:49,878] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:48:49,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934574045.1_ERR7746217_bin.293_genomic.fna/markers.fasta)
[2023-06-04 23:48:49,878] [INFO] Task started: Blastn
[2023-06-04 23:48:49,879] [INFO] Running command: blastn -query GCA_934574045.1_ERR7746217_bin.293_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed22047-4bce-469b-a1ae-34edff198e40/dqc_reference/reference_markers_gtdb.fasta -out GCA_934574045.1_ERR7746217_bin.293_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:51,216] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:51,220] [INFO] Selected 18 target genomes.
[2023-06-04 23:48:51,221] [INFO] Target genome list was writen to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:48:51,229] [INFO] Task started: fastANI
[2023-06-04 23:48:51,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ebfea2-8c56-43ca-8c8a-65b97f5ae1b5/GCA_934574045.1_ERR7746217_bin.293_genomic.fna.gz --refList GCA_934574045.1_ERR7746217_bin.293_genomic.fna/target_genomes_gtdb.txt --output GCA_934574045.1_ERR7746217_bin.293_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:49:00,053] [INFO] Task succeeded: fastANI
[2023-06-04 23:49:00,081] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 23:49:00,081] [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_000307265.1	s__Oscillibacter ruminantium	81.5593	443	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	98.68	98.68	0.93	0.93	2	-
GCF_000283575.1	s__Oscillibacter valericigenes	81.1344	437	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	80.8819	348	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_002455655.1	s__Oscillibacter sp002455655	80.712	355	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228705.1	s__Dysosmobacter sp018228705	80.5447	381	717	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_019118505.1	s__Dysosmobacter excrementavium	80.5295	335	717	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_900544955.1	s__Dysosmobacter sp900544955	80.5136	324	717	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_019118935.1	s__Dysosmobacter pullicola	80.4143	361	717	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_004558115.1	s__Dysosmobacter sp004558115	80.2178	265	717	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_900548505.1	s__Dysosmobacter sp900548505	80.1299	287	717	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_005121165.2	s__Dysosmobacter welbionis	80.0094	360	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCA_017937405.1	s__Dysosmobacter sp017937405	79.7875	308	717	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_000403435.2	s__Dysosmobacter sp000403435	79.6656	343	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCA_910585385.1	s__Dysosmobacter sp910585385	79.605	275	717	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_002392625.1	s__CAG-83 sp002392625	78.5265	164	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.65	99.65	0.89	0.89	2	-
GCA_017458885.1	s__ER4 sp017458885	77.9296	73	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161175.1	s__Lawsonibacter sp002161175	77.7525	123	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784305.1	s__Onthomonas sp902784305	77.252	131	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:49:00,083] [INFO] GTDB search result was written to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/result_gtdb.tsv
[2023-06-04 23:49:00,084] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:49:00,088] [INFO] DFAST_QC result json was written to GCA_934574045.1_ERR7746217_bin.293_genomic.fna/dqc_result.json
[2023-06-04 23:49:00,088] [INFO] DFAST_QC completed!
[2023-06-04 23:49:00,088] [INFO] Total running time: 0h0m49s