[2023-06-13 02:47:54,783] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:47:54,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:47:54,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference
[2023-06-13 02:47:56,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:47:56,163] [INFO] Task started: Prodigal
[2023-06-13 02:47:56,163] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8fa9f18-c5cf-408c-a880-ee15dd407515/GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:48:09,129] [INFO] Task succeeded: Prodigal
[2023-06-13 02:48:09,129] [INFO] Task started: HMMsearch
[2023-06-13 02:48:09,130] [INFO] Running command: hmmsearch --tblout GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/reference_markers.hmm GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:48:09,368] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:48:09,370] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8fa9f18-c5cf-408c-a880-ee15dd407515/GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 02:48:09,396] [INFO] Query marker FASTA was written to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 02:48:09,397] [INFO] Task started: Blastn
[2023-06-13 02:48:09,397] [INFO] Running command: blastn -query GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/reference_markers.fasta -out GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:48:10,002] [INFO] Task succeeded: Blastn
[2023-06-13 02:48:10,006] [INFO] Selected 29 target genomes.
[2023-06-13 02:48:10,007] [INFO] Target genome list was writen to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:48:10,015] [INFO] Task started: fastANI
[2023-06-13 02:48:10,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8fa9f18-c5cf-408c-a880-ee15dd407515/GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:48:28,235] [INFO] Task succeeded: fastANI
[2023-06-13 02:48:28,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:48:28,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:48:28,243] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:48:28,243] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:48:28,243] [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	76.2982	54	690	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:48:28,246] [INFO] DFAST Taxonomy check result was written to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:48:28,247] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:48:28,248] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:48:28,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/checkm_data
[2023-06-13 02:48:28,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:48:28,312] [INFO] Task started: CheckM
[2023-06-13 02:48:28,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 02:49:08,820] [INFO] Task succeeded: CheckM
[2023-06-13 02:49:08,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:49:08,842] [INFO] ===== Completeness check finished =====
[2023-06-13 02:49:08,843] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:49:08,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:49:08,844] [INFO] Task started: Blastn
[2023-06-13 02:49:08,844] [INFO] Running command: blastn -query GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78fdcf1f-443b-45ad-b92a-b4f353eabb09/dqc_reference/reference_markers_gtdb.fasta -out GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:49:09,702] [INFO] Task succeeded: Blastn
[2023-06-13 02:49:09,707] [INFO] Selected 20 target genomes.
[2023-06-13 02:49:09,707] [INFO] Target genome list was writen to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:49:09,716] [INFO] Task started: fastANI
[2023-06-13 02:49:09,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8fa9f18-c5cf-408c-a880-ee15dd407515/GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:49:18,146] [INFO] Task succeeded: fastANI
[2023-06-13 02:49:18,164] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:49:18,165] [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_002491245.1	s__CAG-873 sp002491245	99.8034	551	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.67	97.75	0.93	0.87	9	conclusive
GCA_017620635.1	s__CAG-873 sp017620635	78.5652	262	690	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_910579995.1	s__CAG-873 sp009775135	78.548	210	690	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_004102805.1	s__UBA7173 sp004102805	78.2966	54	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_009775195.1	s__CAG-873 sp009775195	78.2032	206	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.01	95.47	0.84	0.74	3	-
GCA_001689415.1	s__CAG-873 sp001689415	78.1253	185	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.88	97.88	0.88	0.88	2	-
GCA_900759845.1	s__CAG-873 sp900759845	77.6024	132	690	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_009775225.1	s__CAG-873 sp009775225	77.4294	115	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.13	98.13	0.88	0.86	3	-
GCA_900548975.1	s__CAG-873 sp900548975	77.3226	113	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_900555715.1	s__CAG-873 sp900555715	77.2419	93	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.36	96.57	0.81	0.79	3	-
GCA_910578035.1	s__CAG-873 sp910578035	77.1048	98	690	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_910584495.1	s__CAG-873 sp910584495	77.0641	83	690	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_910579035.1	s__CAG-873 sp011959565	77.0347	106	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.99	96.96	0.89	0.75	5	-
GCA_910583525.1	s__CAG-873 sp910583525	77.0311	120	690	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_905202215.1	s__CAG-873 sp905202215	76.7605	111	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.54	98.54	0.91	0.91	2	-
GCA_910587235.1	s__CAG-873 sp910587235	76.6621	69	690	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_900551515.1	s__Paramuribaculum sp900551515	76.1053	53	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:49:18,167] [INFO] GTDB search result was written to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:49:18,167] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:49:18,171] [INFO] DFAST_QC result json was written to GCA_947036375.1_ERR8099107_bin.22_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:49:18,171] [INFO] DFAST_QC completed!
[2023-06-13 02:49:18,171] [INFO] Total running time: 0h1m23s