[2023-06-13 13:25:00,396] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:25:00,398] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:25:00,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference
[2023-06-13 13:25:01,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:25:01,651] [INFO] Task started: Prodigal
[2023-06-13 13:25:01,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg55f3ae27-72c8-499b-b8fe-c631b2692c77/GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:25:17,450] [INFO] Task succeeded: Prodigal
[2023-06-13 13:25:17,451] [INFO] Task started: HMMsearch
[2023-06-13 13:25:17,451] [INFO] Running command: hmmsearch --tblout GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/reference_markers.hmm GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:25:17,703] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:25:17,705] [INFO] Found 6/6 markers.
[2023-06-13 13:25:17,739] [INFO] Query marker FASTA was written to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 13:25:17,739] [INFO] Task started: Blastn
[2023-06-13 13:25:17,739] [INFO] Running command: blastn -query GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/reference_markers.fasta -out GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:25:18,317] [INFO] Task succeeded: Blastn
[2023-06-13 13:25:18,323] [INFO] Selected 26 target genomes.
[2023-06-13 13:25:18,324] [INFO] Target genome list was writen to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 13:25:18,326] [INFO] Task started: fastANI
[2023-06-13 13:25:18,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f3ae27-72c8-499b-b8fe-c631b2692c77/GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:25:32,795] [INFO] Task succeeded: fastANI
[2023-06-13 13:25:32,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:25:32,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:25:32,806] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:25:32,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:25:32,806] [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
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.0878	52	911	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.0726	54	911	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.9624	58	911	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.6993	53	911	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:25:32,809] [INFO] DFAST Taxonomy check result was written to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 13:25:32,810] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:25:32,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:25:32,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/checkm_data
[2023-06-13 13:25:32,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:25:32,843] [INFO] Task started: CheckM
[2023-06-13 13:25:32,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 13:26:20,414] [INFO] Task succeeded: CheckM
[2023-06-13 13:26:20,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:26:20,442] [INFO] ===== Completeness check finished =====
[2023-06-13 13:26:20,443] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:26:20,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 13:26:20,443] [INFO] Task started: Blastn
[2023-06-13 13:26:20,443] [INFO] Running command: blastn -query GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg65404118-c271-4b73-8dcf-9a85db174d05/dqc_reference/reference_markers_gtdb.fasta -out GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:26:21,273] [INFO] Task succeeded: Blastn
[2023-06-13 13:26:21,279] [INFO] Selected 21 target genomes.
[2023-06-13 13:26:21,279] [INFO] Target genome list was writen to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:26:21,280] [INFO] Task started: fastANI
[2023-06-13 13:26:21,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f3ae27-72c8-499b-b8fe-c631b2692c77/GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:26:31,356] [INFO] Task succeeded: fastANI
[2023-06-13 13:26:31,381] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:26:31,381] [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_009775375.1	s__CAG-485 sp009775375	99.9135	863	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.86	99.86	0.92	0.92	2	conclusive
GCA_910588245.1	s__CAG-485 sp910588245	78.6895	275	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.72	98.72	0.89	0.89	2	-
GCA_910585275.1	s__CAG-485 sp910585275	78.0776	240	911	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_014801605.1	s__CAG-485 sp014801605	77.8859	112	911	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_910584125.1	s__CAG-485 sp910584125	77.6104	95	911	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_009775365.1	s__CAG-485 sp009775365	77.6055	173	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.04	99.04	0.86	0.86	2	-
GCA_905209725.1	s__CAG-485 sp900556595	77.5583	89	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.46	99.46	0.94	0.94	2	-
GCA_003762615.1	s__CAG-485 sp002493045	77.478	187	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.48	99.22	0.95	0.91	14	-
GCA_002493515.1	s__CAG-485 sp002493515	77.3964	136	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.64	97.64	0.78	0.78	2	-
GCA_905214735.1	s__CAG-485 sp905214735	77.3292	110	911	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_900554345.1	s__CAG-485 sp900554345	77.2992	97	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.71	99.71	0.77	0.77	2	-
GCA_014801875.1	s__CAG-485 sp014801875	77.2655	109	911	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_910583795.1	s__CAG-485 sp910583795	77.1976	135	911	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_014801595.1	s__CAG-485 sp014801595	77.1473	66	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.47	97.47	0.83	0.83	2	-
GCA_900760815.1	s__CAG-485 sp900760815	77.0658	92	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.28	97.28	0.85	0.85	2	-
GCA_910583775.1	s__CAG-485 sp910583775	76.9959	114	911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:26:31,383] [INFO] GTDB search result was written to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 13:26:31,384] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:26:31,387] [INFO] DFAST_QC result json was written to GCA_947365355.1_SRR16350236_bin.8_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 13:26:31,387] [INFO] DFAST_QC completed!
[2023-06-13 13:26:31,387] [INFO] Total running time: 0h1m31s