[2023-06-30 12:52:39,172] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:52:39,175] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:52:39,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference
[2023-06-30 12:52:42,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:52:42,256] [INFO] Task started: Prodigal
[2023-06-30 12:52:42,256] [INFO] Running command: gunzip -c /var/lib/cwl/stgb278533d-0dfa-4c67-86f3-19c18e2859da/GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna.gz | prodigal -d GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/cds.fna -a GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:52:48,701] [INFO] Task succeeded: Prodigal
[2023-06-30 12:52:48,701] [INFO] Task started: HMMsearch
[2023-06-30 12:52:48,702] [INFO] Running command: hmmsearch --tblout GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/reference_markers.hmm GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:52:49,022] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:52:49,023] [INFO] Found 6/6 markers.
[2023-06-30 12:52:49,056] [INFO] Query marker FASTA was written to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/markers.fasta
[2023-06-30 12:52:49,057] [INFO] Task started: Blastn
[2023-06-30 12:52:49,057] [INFO] Running command: blastn -query GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/markers.fasta -db /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/reference_markers.fasta -out GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:52:49,801] [INFO] Task succeeded: Blastn
[2023-06-30 12:52:49,805] [INFO] Selected 33 target genomes.
[2023-06-30 12:52:49,805] [INFO] Target genome list was writen to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/target_genomes.txt
[2023-06-30 12:52:49,806] [INFO] Task started: fastANI
[2023-06-30 12:52:49,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgb278533d-0dfa-4c67-86f3-19c18e2859da/GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna.gz --refList GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/target_genomes.txt --output GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:53:20,505] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:20,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:53:20,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:53:20,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:53:20,508] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:53:20,508] [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 12:53:20,510] [INFO] DFAST Taxonomy check result was written to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/tc_result.tsv
[2023-06-30 12:53:20,510] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:53:20,510] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:53:20,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/checkm_data
[2023-06-30 12:53:20,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:53:20,545] [INFO] Task started: CheckM
[2023-06-30 12:53:20,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/checkm_input GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/checkm_result
[2023-06-30 12:53:45,687] [INFO] Task succeeded: CheckM
[2023-06-30 12:53:45,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:53:45,709] [INFO] ===== Completeness check finished =====
[2023-06-30 12:53:45,710] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:53:45,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/markers.fasta)
[2023-06-30 12:53:45,711] [INFO] Task started: Blastn
[2023-06-30 12:53:45,711] [INFO] Running command: blastn -query GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/markers.fasta -db /var/lib/cwl/stgd67ea421-c5ff-4c2b-8ee1-d0cc390c87d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:53:46,587] [INFO] Task succeeded: Blastn
[2023-06-30 12:53:46,593] [INFO] Selected 18 target genomes.
[2023-06-30 12:53:46,593] [INFO] Target genome list was writen to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:53:46,595] [INFO] Task started: fastANI
[2023-06-30 12:53:46,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgb278533d-0dfa-4c67-86f3-19c18e2859da/GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna.gz --refList GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/target_genomes_gtdb.txt --output GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:53:54,535] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:54,548] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:53:54,548] [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_903960135.1	s__GCA-2737125 sp903960135	99.7747	622	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	99.76	99.60	0.93	0.90	38	conclusive
GCA_005798555.1	s__GCA-2737125 sp005798555	92.809	521	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	99.66	99.52	0.91	0.89	3	-
GCA_014190275.1	s__GCA-2737125 sp014190275	82.9164	433	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694585.1	s__GCA-2737125 sp009694585	80.7501	305	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702725.1	s__GCA-2737125 sp009702725	80.3788	199	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	97.51	97.34	0.71	0.67	4	-
GCA_009700485.1	s__GCA-2737125 sp009700485	80.3115	238	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737125.1	s__GCA-2737125 sp002737125	80.1429	197	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970025.1	s__REEB460 sp018970025	76.7094	60	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__REEB460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456155.1	s__UBA10649 sp003456155	76.5	56	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856385.1	s__UBA10649 sp017856385	76.3938	70	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	76.2282	70	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849335.1	s__UBA10649 sp017849335	75.6522	52	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:53:54,551] [INFO] GTDB search result was written to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/result_gtdb.tsv
[2023-06-30 12:53:54,551] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:53:54,554] [INFO] DFAST_QC result json was written to GCA_903933415.1_freshwater_MAG_---_Loc090519-7m_bin-0419_genomic.fna/dqc_result.json
[2023-06-30 12:53:54,555] [INFO] DFAST_QC completed!
[2023-06-30 12:53:54,555] [INFO] Total running time: 0h1m15s