[2023-06-17 05:04:41,149] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:04:41,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:04:41,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference
[2023-06-17 05:04:42,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:04:42,576] [INFO] Task started: Prodigal
[2023-06-17 05:04:42,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f01e63c-8b60-454e-afa5-5ae413404cd7/GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna.gz | prodigal -d GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/cds.fna -a GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:04:53,262] [INFO] Task succeeded: Prodigal
[2023-06-17 05:04:53,263] [INFO] Task started: HMMsearch
[2023-06-17 05:04:53,263] [INFO] Running command: hmmsearch --tblout GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/reference_markers.hmm GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:04:53,526] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:04:53,527] [INFO] Found 6/6 markers.
[2023-06-17 05:04:53,554] [INFO] Query marker FASTA was written to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/markers.fasta
[2023-06-17 05:04:53,555] [INFO] Task started: Blastn
[2023-06-17 05:04:53,555] [INFO] Running command: blastn -query GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/markers.fasta -db /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/reference_markers.fasta -out GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:04:54,217] [INFO] Task succeeded: Blastn
[2023-06-17 05:04:54,221] [INFO] Selected 29 target genomes.
[2023-06-17 05:04:54,221] [INFO] Target genome list was writen to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/target_genomes.txt
[2023-06-17 05:04:54,248] [INFO] Task started: fastANI
[2023-06-17 05:04:54,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f01e63c-8b60-454e-afa5-5ae413404cd7/GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna.gz --refList GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/target_genomes.txt --output GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:05:14,594] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:14,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:05:14,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:05:14,601] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:05:14,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 05:05:14,602] [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 muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.305	61	504	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.8258	58	504	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	75.9264	50	504	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 05:05:14,604] [INFO] DFAST Taxonomy check result was written to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/tc_result.tsv
[2023-06-17 05:05:14,605] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:05:14,605] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:05:14,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/checkm_data
[2023-06-17 05:05:14,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:05:14,636] [INFO] Task started: CheckM
[2023-06-17 05:05:14,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/checkm_input GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/checkm_result
[2023-06-17 05:05:48,553] [INFO] Task succeeded: CheckM
[2023-06-17 05:05:48,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 3.12%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:05:48,579] [INFO] ===== Completeness check finished =====
[2023-06-17 05:05:48,580] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:05:48,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/markers.fasta)
[2023-06-17 05:05:48,580] [INFO] Task started: Blastn
[2023-06-17 05:05:48,581] [INFO] Running command: blastn -query GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/markers.fasta -db /var/lib/cwl/stgea73518d-42c1-4f66-80fa-451b85e80ec7/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:05:49,633] [INFO] Task succeeded: Blastn
[2023-06-17 05:05:49,654] [INFO] Selected 12 target genomes.
[2023-06-17 05:05:49,654] [INFO] Target genome list was writen to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:05:49,673] [INFO] Task started: fastANI
[2023-06-17 05:05:49,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f01e63c-8b60-454e-afa5-5ae413404cd7/GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna.gz --refList GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/target_genomes_gtdb.txt --output GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:05:54,781] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:54,795] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:05:54,795] [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_905193995.1	s__CAG-873 sp905193995	100.0	496	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587925.1	s__CAG-873 sp910587925	78.5335	173	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759825.1	s__CAG-873 sp900759825	78.4965	137	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577315.1	s__CAG-873 sp910577315	78.4181	182	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.79	97.79	0.88	0.88	2	-
GCA_905193395.1	s__CAG-873 sp905193395	78.2932	122	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624155.1	s__CAG-873 sp017624155	78.2435	147	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577355.1	s__CAG-873 sp910577355	78.0548	144	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552485.1	s__CAG-873 sp004552485	77.9188	123	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.38	99.38	0.89	0.89	2	-
GCA_900550395.1	s__CAG-873 sp900550395	77.5304	106	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.34	95.74	0.88	0.82	4	-
GCA_001689495.1	s__Duncaniella sp001689495	77.4345	110	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCA_910586975.1	s__CAG-873 sp910586975	77.2956	103	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	77.2822	85	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 05:05:54,797] [INFO] GTDB search result was written to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/result_gtdb.tsv
[2023-06-17 05:05:54,798] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:05:54,801] [INFO] DFAST_QC result json was written to GCA_905193995.1_ERR1190813-mag-bin.32_genomic.fna/dqc_result.json
[2023-06-17 05:05:54,801] [INFO] DFAST_QC completed!
[2023-06-17 05:05:54,801] [INFO] Total running time: 0h1m14s