[2023-06-30 04:51:18,058] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:51:18,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:51:18,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference
[2023-06-30 04:51:19,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:51:19,868] [INFO] Task started: Prodigal
[2023-06-30 04:51:19,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg695b0005-f4e4-4fde-b9fd-6004aae4f058/GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna.gz | prodigal -d GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/cds.fna -a GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:51:22,061] [INFO] Task succeeded: Prodigal
[2023-06-30 04:51:22,062] [INFO] Task started: HMMsearch
[2023-06-30 04:51:22,062] [INFO] Running command: hmmsearch --tblout GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/reference_markers.hmm GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:51:22,305] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:51:22,306] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg695b0005-f4e4-4fde-b9fd-6004aae4f058/GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna.gz]
[2023-06-30 04:51:22,319] [INFO] Query marker FASTA was written to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/markers.fasta
[2023-06-30 04:51:22,320] [INFO] Task started: Blastn
[2023-06-30 04:51:22,320] [INFO] Running command: blastn -query GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/reference_markers.fasta -out GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:51:22,913] [INFO] Task succeeded: Blastn
[2023-06-30 04:51:22,916] [INFO] Selected 15 target genomes.
[2023-06-30 04:51:22,917] [INFO] Target genome list was writen to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/target_genomes.txt
[2023-06-30 04:51:22,920] [INFO] Task started: fastANI
[2023-06-30 04:51:22,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg695b0005-f4e4-4fde-b9fd-6004aae4f058/GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna.gz --refList GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/target_genomes.txt --output GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:51:29,434] [INFO] Task succeeded: fastANI
[2023-06-30 04:51:29,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:51:29,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:51:29,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:51:29,438] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:51:29,438] [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 04:51:29,440] [INFO] DFAST Taxonomy check result was written to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/tc_result.tsv
[2023-06-30 04:51:29,440] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:51:29,440] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:51:29,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/checkm_data
[2023-06-30 04:51:29,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:51:29,462] [INFO] Task started: CheckM
[2023-06-30 04:51:29,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/checkm_input GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/checkm_result
[2023-06-30 04:51:45,178] [INFO] Task succeeded: CheckM
[2023-06-30 04:51:45,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.55%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 04:51:45,213] [INFO] ===== Completeness check finished =====
[2023-06-30 04:51:45,213] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:51:45,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/markers.fasta)
[2023-06-30 04:51:45,213] [INFO] Task started: Blastn
[2023-06-30 04:51:45,214] [INFO] Running command: blastn -query GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9bb9d24-f1be-4bfb-b87a-807a88674ba2/dqc_reference/reference_markers_gtdb.fasta -out GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:51:45,747] [INFO] Task succeeded: Blastn
[2023-06-30 04:51:45,752] [INFO] Selected 11 target genomes.
[2023-06-30 04:51:45,753] [INFO] Target genome list was writen to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:51:45,762] [INFO] Task started: fastANI
[2023-06-30 04:51:45,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg695b0005-f4e4-4fde-b9fd-6004aae4f058/GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna.gz --refList GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/target_genomes_gtdb.txt --output GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:51:48,643] [INFO] Task succeeded: fastANI
[2023-06-30 04:51:48,656] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:51:48,656] [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_903891755.1	s__PALSA-747 sp903891755	97.1281	124	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.94	98.90	0.76	0.73	3	conclusive
GCA_903932705.1	s__PALSA-747 sp903932705	87.3744	102	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842855.1	s__PALSA-747 sp903842855	79.986	56	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916385.1	s__PALSA-747 sp903916385	79.5873	67	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.45	98.98	0.86	0.80	10	-
GCA_903827345.1	s__PALSA-747 sp903827345	78.6986	57	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	97.69	97.69	0.77	0.77	2	-
GCA_903899375.1	s__PALSA-747 sp903899375	78.49	66	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.46	99.00	0.86	0.79	59	-
GCA_903933585.1	s__PALSA-747 sp903933585	78.3744	64	160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.42	99.37	0.91	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-30 04:51:48,659] [INFO] GTDB search result was written to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/result_gtdb.tsv
[2023-06-30 04:51:48,660] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:51:48,663] [INFO] DFAST_QC result json was written to GCA_903825175.1_freshwater_MAG_---_VK_bin-4594_genomic.fna/dqc_result.json
[2023-06-30 04:51:48,663] [INFO] DFAST_QC completed!
[2023-06-30 04:51:48,663] [INFO] Total running time: 0h0m31s