[2023-06-29 23:48:26,107] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:48:26,109] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:48:26,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference
[2023-06-29 23:48:27,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:48:27,391] [INFO] Task started: Prodigal
[2023-06-29 23:48:27,391] [INFO] Running command: gunzip -c /var/lib/cwl/stge45be7ae-d76b-486b-9cf8-bcb011011172/GCA_900752175.1_ERS235564_41_genomic.fna.gz | prodigal -d GCA_900752175.1_ERS235564_41_genomic.fna/cds.fna -a GCA_900752175.1_ERS235564_41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:48:47,082] [INFO] Task succeeded: Prodigal
[2023-06-29 23:48:47,083] [INFO] Task started: HMMsearch
[2023-06-29 23:48:47,083] [INFO] Running command: hmmsearch --tblout GCA_900752175.1_ERS235564_41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/reference_markers.hmm GCA_900752175.1_ERS235564_41_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:48:47,338] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:48:47,340] [INFO] Found 6/6 markers.
[2023-06-29 23:48:47,372] [INFO] Query marker FASTA was written to GCA_900752175.1_ERS235564_41_genomic.fna/markers.fasta
[2023-06-29 23:48:47,372] [INFO] Task started: Blastn
[2023-06-29 23:48:47,372] [INFO] Running command: blastn -query GCA_900752175.1_ERS235564_41_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/reference_markers.fasta -out GCA_900752175.1_ERS235564_41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:48:48,005] [INFO] Task succeeded: Blastn
[2023-06-29 23:48:48,010] [INFO] Selected 26 target genomes.
[2023-06-29 23:48:48,010] [INFO] Target genome list was writen to GCA_900752175.1_ERS235564_41_genomic.fna/target_genomes.txt
[2023-06-29 23:48:48,012] [INFO] Task started: fastANI
[2023-06-29 23:48:48,012] [INFO] Running command: fastANI --query /var/lib/cwl/stge45be7ae-d76b-486b-9cf8-bcb011011172/GCA_900752175.1_ERS235564_41_genomic.fna.gz --refList GCA_900752175.1_ERS235564_41_genomic.fna/target_genomes.txt --output GCA_900752175.1_ERS235564_41_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:49:01,999] [INFO] Task succeeded: fastANI
[2023-06-29 23:49:01,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:49:02,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:49:02,010] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:49:02,011] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:49:02,011] [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
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	78.1667	90	1100	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.7316	79	1100	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.6558	77	1100	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.6522	80	1100	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.6072	81	1100	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.4287	67	1100	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	76.3465	69	1100	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.0881	55	1100	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:49:02,013] [INFO] DFAST Taxonomy check result was written to GCA_900752175.1_ERS235564_41_genomic.fna/tc_result.tsv
[2023-06-29 23:49:02,013] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:49:02,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:49:02,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/checkm_data
[2023-06-29 23:49:02,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:49:02,055] [INFO] Task started: CheckM
[2023-06-29 23:49:02,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752175.1_ERS235564_41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752175.1_ERS235564_41_genomic.fna/checkm_input GCA_900752175.1_ERS235564_41_genomic.fna/checkm_result
[2023-06-29 23:49:57,352] [INFO] Task succeeded: CheckM
[2023-06-29 23:49:57,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:49:57,374] [INFO] ===== Completeness check finished =====
[2023-06-29 23:49:57,374] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:49:57,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752175.1_ERS235564_41_genomic.fna/markers.fasta)
[2023-06-29 23:49:57,375] [INFO] Task started: Blastn
[2023-06-29 23:49:57,375] [INFO] Running command: blastn -query GCA_900752175.1_ERS235564_41_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a5798b-2fe1-486a-810f-56c471a8f12e/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752175.1_ERS235564_41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:49:58,202] [INFO] Task succeeded: Blastn
[2023-06-29 23:49:58,207] [INFO] Selected 6 target genomes.
[2023-06-29 23:49:58,207] [INFO] Target genome list was writen to GCA_900752175.1_ERS235564_41_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:49:58,209] [INFO] Task started: fastANI
[2023-06-29 23:49:58,209] [INFO] Running command: fastANI --query /var/lib/cwl/stge45be7ae-d76b-486b-9cf8-bcb011011172/GCA_900752175.1_ERS235564_41_genomic.fna.gz --refList GCA_900752175.1_ERS235564_41_genomic.fna/target_genomes_gtdb.txt --output GCA_900752175.1_ERS235564_41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:50:02,735] [INFO] Task succeeded: fastANI
[2023-06-29 23:50:02,749] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:50:02,749] [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_900760735.1	s__CAG-485 sp900760735	95.0419	855	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	95.21	95.16	0.81	0.77	3	conclusive
GCA_905198125.1	s__CAG-485 sp905198125	93.9337	804	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542185.1	s__CAG-485 sp900542185	93.3055	817	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361235.1	s__CAG-485 sp002361235	92.8631	726	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.58	98.09	0.93	0.87	10	-
GCA_902796035.1	s__CAG-485 sp900321585	91.8874	603	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.23	95.66	0.86	0.76	5	-
GCA_900759795.1	s__CAG-485 sp900759795	79.8175	285	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:50:02,752] [INFO] GTDB search result was written to GCA_900752175.1_ERS235564_41_genomic.fna/result_gtdb.tsv
[2023-06-29 23:50:02,753] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:50:02,757] [INFO] DFAST_QC result json was written to GCA_900752175.1_ERS235564_41_genomic.fna/dqc_result.json
[2023-06-29 23:50:02,758] [INFO] DFAST_QC completed!
[2023-06-29 23:50:02,758] [INFO] Total running time: 0h1m37s