[2023-06-13 04:36:00,583] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:36:00,588] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:36:00,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference
[2023-06-13 04:36:01,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:36:01,832] [INFO] Task started: Prodigal
[2023-06-13 04:36:01,832] [INFO] Running command: gunzip -c /var/lib/cwl/stga6011ec4-468d-4be4-bb48-497d68782c88/GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:36:06,460] [INFO] Task succeeded: Prodigal
[2023-06-13 04:36:06,460] [INFO] Task started: HMMsearch
[2023-06-13 04:36:06,460] [INFO] Running command: hmmsearch --tblout GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/reference_markers.hmm GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:36:06,668] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:36:06,669] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga6011ec4-468d-4be4-bb48-497d68782c88/GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 04:36:06,698] [INFO] Query marker FASTA was written to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 04:36:06,699] [INFO] Task started: Blastn
[2023-06-13 04:36:06,699] [INFO] Running command: blastn -query GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/reference_markers.fasta -out GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:07,203] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:07,208] [INFO] Selected 10 target genomes.
[2023-06-13 04:36:07,209] [INFO] Target genome list was writen to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 04:36:07,211] [INFO] Task started: fastANI
[2023-06-13 04:36:07,211] [INFO] Running command: fastANI --query /var/lib/cwl/stga6011ec4-468d-4be4-bb48-497d68782c88/GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:36:11,236] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:11,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:36:11,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:36:11,245] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:36:11,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:36:11,246] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.2555	55	491	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.0964	53	491	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.0071	53	491	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.9415	70	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:36:11,248] [INFO] DFAST Taxonomy check result was written to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 04:36:11,249] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:36:11,249] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:36:11,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/checkm_data
[2023-06-13 04:36:11,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:36:11,278] [INFO] Task started: CheckM
[2023-06-13 04:36:11,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 04:36:31,965] [INFO] Task succeeded: CheckM
[2023-06-13 04:36:31,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.70%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:36:31,994] [INFO] ===== Completeness check finished =====
[2023-06-13 04:36:31,995] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:36:31,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 04:36:31,996] [INFO] Task started: Blastn
[2023-06-13 04:36:31,996] [INFO] Running command: blastn -query GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8153e2d6-e3b6-45cb-8f0a-aae04f2ab957/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:32,591] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:32,595] [INFO] Selected 13 target genomes.
[2023-06-13 04:36:32,596] [INFO] Target genome list was writen to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:36:32,597] [INFO] Task started: fastANI
[2023-06-13 04:36:32,598] [INFO] Running command: fastANI --query /var/lib/cwl/stga6011ec4-468d-4be4-bb48-497d68782c88/GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:36:37,856] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:37,867] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:36:37,868] [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_018711755.1	s__Limivicinus faecipullorum	97.307	351	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900754515.1	s__Limivicinus sp900754515	83.4497	330	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.83	97.83	0.85	0.85	2	-
GCA_004560305.1	s__Limivicinus sp004560305	81.5404	201	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	96.68	96.68	0.69	0.69	2	-
GCA_017470325.1	s__Limivicinus sp017470325	78.7381	131	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545165.1	s__Limivicinus sp017545165	78.6857	115	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	78.5867	148	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319835.1	s__Limivicinus sp900319835	78.4596	143	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902765595.1	s__Limivicinus sp002350825	78.3784	140	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_902778275.1	s__Limivicinus sp902778275	78.3256	151	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319635.1	s__Limivicinus sp900319635	78.1685	140	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_900316255.1	s__Limivicinus sp900316255	78.118	144	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.92	95.41	0.88	0.79	4	-
GCA_002320035.1	s__Limivicinus sp002320035	77.5966	115	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.95	98.71	0.80	0.75	5	-
--------------------------------------------------------------------------------
[2023-06-13 04:36:37,870] [INFO] GTDB search result was written to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 04:36:37,871] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:36:37,875] [INFO] DFAST_QC result json was written to GCA_938005295.1_ERR912108_bin.110_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 04:36:37,875] [INFO] DFAST_QC completed!
[2023-06-13 04:36:37,875] [INFO] Total running time: 0h0m37s