[2023-06-05 01:31:44,956] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:31:44,961] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:31:44,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference
[2023-06-05 01:31:46,305] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:31:46,306] [INFO] Task started: Prodigal
[2023-06-05 01:31:46,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg10931a69-8dcd-496d-9179-45d1443b0aa2/GCA_934828805.1_MTG221_bin.13.fa_genomic.fna.gz | prodigal -d GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/cds.fna -a GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:32:09,068] [INFO] Task succeeded: Prodigal
[2023-06-05 01:32:09,069] [INFO] Task started: HMMsearch
[2023-06-05 01:32:09,069] [INFO] Running command: hmmsearch --tblout GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/reference_markers.hmm GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:32:09,378] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:32:09,379] [INFO] Found 6/6 markers.
[2023-06-05 01:32:09,422] [INFO] Query marker FASTA was written to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/markers.fasta
[2023-06-05 01:32:09,422] [INFO] Task started: Blastn
[2023-06-05 01:32:09,422] [INFO] Running command: blastn -query GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/reference_markers.fasta -out GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:32:10,029] [INFO] Task succeeded: Blastn
[2023-06-05 01:32:10,033] [INFO] Selected 15 target genomes.
[2023-06-05 01:32:10,034] [INFO] Target genome list was writen to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/target_genomes.txt
[2023-06-05 01:32:10,035] [INFO] Task started: fastANI
[2023-06-05 01:32:10,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg10931a69-8dcd-496d-9179-45d1443b0aa2/GCA_934828805.1_MTG221_bin.13.fa_genomic.fna.gz --refList GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/target_genomes.txt --output GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:32:21,197] [INFO] Task succeeded: fastANI
[2023-06-05 01:32:21,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:32:21,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:32:21,212] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2023-06-05 01:32:21,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 01:32:21,213] [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
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	99.1211	1372	1525	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	99.0759	1373	1525	95	conclusive
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	99.0586	1377	1525	95	conclusive
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	78.3146	303	1525	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.9883	315	1525	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.9882	315	1525	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	77.9574	294	1525	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.844	301	1525	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.8044	313	1525	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	76.3133	52	1525	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:32:21,215] [INFO] DFAST Taxonomy check result was written to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/tc_result.tsv
[2023-06-05 01:32:21,216] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:32:21,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:32:21,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/checkm_data
[2023-06-05 01:32:21,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:32:21,263] [INFO] Task started: CheckM
[2023-06-05 01:32:21,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/checkm_input GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/checkm_result
[2023-06-05 01:33:23,608] [INFO] Task succeeded: CheckM
[2023-06-05 01:33:23,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:33:23,633] [INFO] ===== Completeness check finished =====
[2023-06-05 01:33:23,633] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:33:23,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/markers.fasta)
[2023-06-05 01:33:23,634] [INFO] Task started: Blastn
[2023-06-05 01:33:23,634] [INFO] Running command: blastn -query GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0bbd6f-d7b0-4fbe-a5c3-553e7daed85f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:33:24,414] [INFO] Task succeeded: Blastn
[2023-06-05 01:33:24,420] [INFO] Selected 22 target genomes.
[2023-06-05 01:33:24,420] [INFO] Target genome list was writen to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:33:24,482] [INFO] Task started: fastANI
[2023-06-05 01:33:24,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg10931a69-8dcd-496d-9179-45d1443b0aa2/GCA_934828805.1_MTG221_bin.13.fa_genomic.fna.gz --refList GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:33:38,355] [INFO] Task succeeded: fastANI
[2023-06-05 01:33:38,369] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:33:38,370] [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_000012845.1	s__Parabacteroides distasonis	99.0776	1372	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	conclusive
GCF_004793765.1	s__Parabacteroides distasonis_A	94.152	942	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	89.9799	751	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003150615.1	s__Merdimorpha sp003150615	88.4781	52	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA1820;g__Merdimorpha	95.0	98.91	98.71	0.82	0.79	8	-
GCF_015550595.1	s__Parabacteroides sp900540715	78.3024	306	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_905196875.1	s__Parabacteroides sp905196875	78.0403	270	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.9882	312	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCF_014287585.1	s__Parabacteroides sp014287585	77.9391	328	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.9327	295	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.8161	285	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.7952	312	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_900770835.1	s__Parabacteroides sp900770835	77.7557	218	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.5379	266	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.2387	149	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
GCF_012113595.1	s__Bacteroides sp012113595	76.4613	53	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:33:38,374] [INFO] GTDB search result was written to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 01:33:38,374] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:33:38,380] [INFO] DFAST_QC result json was written to GCA_934828805.1_MTG221_bin.13.fa_genomic.fna/dqc_result.json
[2023-06-05 01:33:38,380] [INFO] DFAST_QC completed!
[2023-06-05 01:33:38,380] [INFO] Total running time: 0h1m53s