[2023-06-13 02:18:16,810] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:18:16,812] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:18:16,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference
[2023-06-13 02:18:19,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:18:19,761] [INFO] Task started: Prodigal
[2023-06-13 02:18:19,762] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc157cc9-7ff9-4a50-8461-5cb41fe8c3f0/GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:18:24,208] [INFO] Task succeeded: Prodigal
[2023-06-13 02:18:24,209] [INFO] Task started: HMMsearch
[2023-06-13 02:18:24,209] [INFO] Running command: hmmsearch --tblout GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/reference_markers.hmm GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:18:24,546] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:18:24,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc157cc9-7ff9-4a50-8461-5cb41fe8c3f0/GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 02:18:24,579] [INFO] Query marker FASTA was written to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 02:18:24,580] [INFO] Task started: Blastn
[2023-06-13 02:18:24,580] [INFO] Running command: blastn -query GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/reference_markers.fasta -out GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:18:26,026] [INFO] Task succeeded: Blastn
[2023-06-13 02:18:26,030] [INFO] Selected 21 target genomes.
[2023-06-13 02:18:26,030] [INFO] Target genome list was writen to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:18:26,033] [INFO] Task started: fastANI
[2023-06-13 02:18:26,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc157cc9-7ff9-4a50-8461-5cb41fe8c3f0/GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:18:40,006] [INFO] Task succeeded: fastANI
[2023-06-13 02:18:40,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:18:40,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:18:40,008] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:18:40,008] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:18:40,008] [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
--------------------------------------------------------------------------------
[2023-06-13 02:18:40,010] [INFO] DFAST Taxonomy check result was written to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:18:40,011] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:18:40,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:18:40,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/checkm_data
[2023-06-13 02:18:40,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:18:40,036] [INFO] Task started: CheckM
[2023-06-13 02:18:40,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 02:19:02,194] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:02,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:02,217] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:02,218] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:02,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:19:02,218] [INFO] Task started: Blastn
[2023-06-13 02:19:02,219] [INFO] Running command: blastn -query GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e80a7a0-35c8-4219-b665-8522a14ff7ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:03,099] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:03,104] [INFO] Selected 20 target genomes.
[2023-06-13 02:19:03,104] [INFO] Target genome list was writen to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:03,159] [INFO] Task started: fastANI
[2023-06-13 02:19:03,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc157cc9-7ff9-4a50-8461-5cb41fe8c3f0/GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:14,545] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:14,561] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:19:14,562] [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_910586025.1	s__CAG-95 sp910586025	99.2054	514	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910579685.1	s__CAG-95 sp910579685	82.008	391	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579425.1	s__CAG-95 sp910579425	77.3424	132	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621815.1	s__CAG-95 sp017621815	76.9365	132	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436115.1	s__CAG-95 sp000436115	76.4812	72	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
GCA_910587305.1	s__CAG-95 sp910587305	76.4169	73	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579495.1	s__CAG-95 sp910579495	76.4101	81	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577445.1	s__CAG-95 sp910577445	76.3757	98	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579755.1	s__Acetatifactor sp910579755	76.3726	63	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492465.1	s__CAG-95 sp002492465	76.3339	92	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621075.1	s__Acetatifactor sp017621075	75.9104	51	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:14,564] [INFO] GTDB search result was written to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:14,564] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:14,567] [INFO] DFAST_QC result json was written to GCA_947170545.1_SRR14862897_bin.32_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:19:14,567] [INFO] DFAST_QC completed!
[2023-06-13 02:19:14,567] [INFO] Total running time: 0h0m58s