[2023-06-16 20:51:13,899] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:51:13,901] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:51:13,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference
[2023-06-16 20:51:15,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:51:15,023] [INFO] Task started: Prodigal
[2023-06-16 20:51:15,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c5e6636-0f89-4dab-b904-2071e7db70c6/GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna.gz | prodigal -d GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/cds.fna -a GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:51:26,164] [INFO] Task succeeded: Prodigal
[2023-06-16 20:51:26,165] [INFO] Task started: HMMsearch
[2023-06-16 20:51:26,165] [INFO] Running command: hmmsearch --tblout GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/reference_markers.hmm GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:51:26,350] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:51:26,351] [INFO] Found 6/6 markers.
[2023-06-16 20:51:26,371] [INFO] Query marker FASTA was written to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/markers.fasta
[2023-06-16 20:51:26,371] [INFO] Task started: Blastn
[2023-06-16 20:51:26,371] [INFO] Running command: blastn -query GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/reference_markers.fasta -out GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:26,928] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:26,931] [INFO] Selected 28 target genomes.
[2023-06-16 20:51:26,932] [INFO] Target genome list was writen to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/target_genomes.txt
[2023-06-16 20:51:26,940] [INFO] Task started: fastANI
[2023-06-16 20:51:26,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5e6636-0f89-4dab-b904-2071e7db70c6/GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna.gz --refList GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/target_genomes.txt --output GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:51:42,645] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:42,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:51:42,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:51:42,653] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:51:42,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:51:42,653] [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
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	78.1022	78	739	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.7311	132	739	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.7101	108	739	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.5993	81	739	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.5382	109	739	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.4252	110	739	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	77.2917	108	739	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.1468	109	739	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.4115	61	739	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:51:42,655] [INFO] DFAST Taxonomy check result was written to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/tc_result.tsv
[2023-06-16 20:51:42,655] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:51:42,655] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:51:42,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/checkm_data
[2023-06-16 20:51:42,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:51:42,682] [INFO] Task started: CheckM
[2023-06-16 20:51:42,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/checkm_input GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/checkm_result
[2023-06-16 20:52:17,577] [INFO] Task succeeded: CheckM
[2023-06-16 20:52:17,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:52:17,594] [INFO] ===== Completeness check finished =====
[2023-06-16 20:52:17,595] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:52:17,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/markers.fasta)
[2023-06-16 20:52:17,596] [INFO] Task started: Blastn
[2023-06-16 20:52:17,596] [INFO] Running command: blastn -query GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stg21794d2b-144f-4977-8465-ef03243dba93/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:52:18,518] [INFO] Task succeeded: Blastn
[2023-06-16 20:52:18,522] [INFO] Selected 15 target genomes.
[2023-06-16 20:52:18,522] [INFO] Target genome list was writen to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:52:18,546] [INFO] Task started: fastANI
[2023-06-16 20:52:18,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5e6636-0f89-4dab-b904-2071e7db70c6/GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna.gz --refList GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/target_genomes_gtdb.txt --output GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:52:25,793] [INFO] Task succeeded: fastANI
[2023-06-16 20:52:25,802] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:52:25,803] [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_001701135.1	s__UBA7173 sp001701135	97.9008	637	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.33	96.66	0.85	0.83	3	conclusive
GCA_910575615.1	s__UBA7173 sp001689685	79.0435	290	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.70	99.58	0.97	0.94	9	-
GCA_004557825.1	s__UBA7173 sp004557825	78.9901	270	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584365.1	s__UBA7173 sp910584365	78.632	258	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759895.1	s__UBA7173 sp900759895	78.5901	148	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207535.1	s__UBA7173 sp905207535	78.5485	214	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548705.1	s__UBA7173 sp900548705	78.4705	240	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.21	98.17	0.86	0.81	4	-
GCA_910587075.1	s__UBA7173 sp910587075	78.1033	206	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540205.1	s__UBA7173 sp900540205	77.9959	183	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.71	95.96	0.83	0.74	4	-
GCA_900551515.1	s__Paramuribaculum sp900551515	77.879	102	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	77.5996	154	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584735.1	s__UBA7173 sp910584735	77.3883	130	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802345.1	s__Duncaniella sp014802345	77.2595	83	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	-
GCA_910579995.1	s__CAG-873 sp009775135	77.1718	106	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.96	0.96	2	-
GCA_910579185.1	s__Paramuribaculum sp910579185	76.7992	87	739	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:52:25,804] [INFO] GTDB search result was written to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/result_gtdb.tsv
[2023-06-16 20:52:25,805] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:52:25,808] [INFO] DFAST_QC result json was written to GCA_905201335.1_ERR414285-mag-bin.18_genomic.fna/dqc_result.json
[2023-06-16 20:52:25,808] [INFO] DFAST_QC completed!
[2023-06-16 20:52:25,808] [INFO] Total running time: 0h1m12s