[2023-06-19 05:24:52,166] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:24:52,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:24:52,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference
[2023-06-19 05:24:54,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:24:54,559] [INFO] Task started: Prodigal
[2023-06-19 05:24:54,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg8339e908-3d20-47d2-a320-fa637a99a5a6/GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:00,146] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:00,146] [INFO] Task started: HMMsearch
[2023-06-19 05:25:00,146] [INFO] Running command: hmmsearch --tblout GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/reference_markers.hmm GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:00,402] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:00,404] [INFO] Found 6/6 markers.
[2023-06-19 05:25:00,433] [INFO] Query marker FASTA was written to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 05:25:00,434] [INFO] Task started: Blastn
[2023-06-19 05:25:00,434] [INFO] Running command: blastn -query GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/reference_markers.fasta -out GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:01,110] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:01,114] [INFO] Selected 31 target genomes.
[2023-06-19 05:25:01,114] [INFO] Target genome list was writen to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 05:25:01,121] [INFO] Task started: fastANI
[2023-06-19 05:25:01,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg8339e908-3d20-47d2-a320-fa637a99a5a6/GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:20,060] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:20,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:20,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:20,075] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:20,075] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:25:20,075] [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
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.5072	135	677	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.453	92	677	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.4508	94	677	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.4284	93	677	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.24	64	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:25:20,078] [INFO] DFAST Taxonomy check result was written to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 05:25:20,080] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:20,081] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:20,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/checkm_data
[2023-06-19 05:25:20,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:20,118] [INFO] Task started: CheckM
[2023-06-19 05:25:20,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 05:25:43,786] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:43,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.55%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:43,823] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:43,823] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:43,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 05:25:43,824] [INFO] Task started: Blastn
[2023-06-19 05:25:43,824] [INFO] Running command: blastn -query GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0480e610-cc1b-4a67-a638-70e88b482fce/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:44,920] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:44,926] [INFO] Selected 32 target genomes.
[2023-06-19 05:25:44,926] [INFO] Target genome list was writen to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:44,954] [INFO] Task started: fastANI
[2023-06-19 05:25:44,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg8339e908-3d20-47d2-a320-fa637a99a5a6/GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:26:03,755] [INFO] Task succeeded: fastANI
[2023-06-19 05:26:03,764] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 05:26:03,765] [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_910577925.1	s__Roseburia sp910577925	77.0997	157	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587865.1	s__Roseburia sp910587865	76.9384	168	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804775.1	s__Roseburia sp014804775	76.6774	103	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937095.1	s__Roseburia sp017937095	76.6307	158	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225345.1	s__Roseburia hominis	76.5072	135	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_900537995.1	s__Roseburia intestinalis	76.4043	93	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_003470905.1	s__Roseburia sp003470905	76.3487	83	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_905206195.1	s__Roseburia sp905206195	76.1845	68	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000174195.1	s__Roseburia inulinivorans	76.129	63	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_900550935.1	s__Roseburia sp900550935	75.9651	61	677	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-19 05:26:03,767] [INFO] GTDB search result was written to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 05:26:03,768] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:26:03,775] [INFO] DFAST_QC result json was written to GCA_937906565.1_ERR982818_bin.21_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 05:26:03,775] [INFO] DFAST_QC completed!
[2023-06-19 05:26:03,775] [INFO] Total running time: 0h1m12s