[2023-06-30 04:11:38,922] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:11:38,924] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:11:38,924] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference
[2023-06-30 04:11:40,395] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:11:40,396] [INFO] Task started: Prodigal
[2023-06-30 04:11:40,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bab80d1-0d7d-45de-863a-f6830fdd3b1c/GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:11:47,673] [INFO] Task succeeded: Prodigal
[2023-06-30 04:11:47,674] [INFO] Task started: HMMsearch
[2023-06-30 04:11:47,674] [INFO] Running command: hmmsearch --tblout GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/reference_markers.hmm GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:11:47,956] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:11:47,957] [INFO] Found 6/6 markers.
[2023-06-30 04:11:47,996] [INFO] Query marker FASTA was written to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 04:11:47,997] [INFO] Task started: Blastn
[2023-06-30 04:11:47,997] [INFO] Running command: blastn -query GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/reference_markers.fasta -out GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:11:48,577] [INFO] Task succeeded: Blastn
[2023-06-30 04:11:48,582] [INFO] Selected 19 target genomes.
[2023-06-30 04:11:48,583] [INFO] Target genome list was writen to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 04:11:48,585] [INFO] Task started: fastANI
[2023-06-30 04:11:48,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bab80d1-0d7d-45de-863a-f6830fdd3b1c/GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:12:03,345] [INFO] Task succeeded: fastANI
[2023-06-30 04:12:03,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:12:03,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:12:03,347] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:12:03,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:12:03,348] [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
--------------------------------------------------------------------------------
[2023-06-30 04:12:03,350] [INFO] DFAST Taxonomy check result was written to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 04:12:03,350] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:12:03,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:12:03,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/checkm_data
[2023-06-30 04:12:03,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:12:03,400] [INFO] Task started: CheckM
[2023-06-30 04:12:03,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 04:12:31,002] [INFO] Task succeeded: CheckM
[2023-06-30 04:12:31,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:12:31,028] [INFO] ===== Completeness check finished =====
[2023-06-30 04:12:31,028] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:12:31,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 04:12:31,029] [INFO] Task started: Blastn
[2023-06-30 04:12:31,029] [INFO] Running command: blastn -query GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc83b2b1-539f-40ff-a22b-3d3b3025d6d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:12:31,856] [INFO] Task succeeded: Blastn
[2023-06-30 04:12:31,861] [INFO] Selected 17 target genomes.
[2023-06-30 04:12:31,861] [INFO] Target genome list was writen to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:12:31,871] [INFO] Task started: fastANI
[2023-06-30 04:12:31,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bab80d1-0d7d-45de-863a-f6830fdd3b1c/GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:12:43,042] [INFO] Task succeeded: fastANI
[2023-06-30 04:12:43,055] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 04:12:43,056] [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_902786505.1	s__RUG369 sp902786505	94.7405	770	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	98.19	98.15	0.84	0.78	8	-
GCA_017550965.1	s__RUG369 sp017550965	78.4956	341	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017441605.1	s__RUG369 sp017441605	77.5618	217	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317365.1	s__RUG369 sp900317365	77.0148	197	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902803085.1	s__RUG369 sp902803085	76.9723	132	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	98.60	98.60	0.97	0.97	2	-
GCA_017937685.1	s__RUG369 sp017937685	76.7831	156	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017466305.1	s__RUG369 sp017466305	76.6452	132	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559825.1	s__RUG369 sp017559825	76.6401	182	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435375.1	s__RUG369 sp017435375	76.6098	162	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318195.1	s__RUG369 sp900318195	76.5666	139	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017937485.1	s__RUG369 sp017937485	76.491	189	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549085.1	s__RUG369 sp017549085	76.4315	101	1103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:12:43,059] [INFO] GTDB search result was written to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 04:12:43,060] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:12:43,064] [INFO] DFAST_QC result json was written to GCA_946541595.1_SRR873597_bin.58_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 04:12:43,064] [INFO] DFAST_QC completed!
[2023-06-30 04:12:43,065] [INFO] Total running time: 0h1m4s