[2023-03-14 13:19:07,356] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:19:07,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:19:07,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference
[2023-03-14 13:19:08,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:19:08,506] [INFO] Task started: Prodigal
[2023-03-14 13:19:08,506] [INFO] Running command: cat /var/lib/cwl/stg39ffa30f-ca48-4aad-b6c0-c1dbff086926/OceanDNA-b7639.fa | prodigal -d OceanDNA-b7639/cds.fna -a OceanDNA-b7639/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:19:17,940] [INFO] Task succeeded: Prodigal
[2023-03-14 13:19:17,940] [INFO] Task started: HMMsearch
[2023-03-14 13:19:17,940] [INFO] Running command: hmmsearch --tblout OceanDNA-b7639/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/reference_markers.hmm OceanDNA-b7639/protein.faa > /dev/null
[2023-03-14 13:19:18,214] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:19:18,215] [INFO] Found 6/6 markers.
[2023-03-14 13:19:18,229] [INFO] Query marker FASTA was written to OceanDNA-b7639/markers.fasta
[2023-03-14 13:19:18,230] [INFO] Task started: Blastn
[2023-03-14 13:19:18,230] [INFO] Running command: blastn -query OceanDNA-b7639/markers.fasta -db /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/reference_markers.fasta -out OceanDNA-b7639/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:19:18,815] [INFO] Task succeeded: Blastn
[2023-03-14 13:19:18,817] [INFO] Selected 32 target genomes.
[2023-03-14 13:19:18,817] [INFO] Target genome list was writen to OceanDNA-b7639/target_genomes.txt
[2023-03-14 13:19:18,828] [INFO] Task started: fastANI
[2023-03-14 13:19:18,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ffa30f-ca48-4aad-b6c0-c1dbff086926/OceanDNA-b7639.fa --refList OceanDNA-b7639/target_genomes.txt --output OceanDNA-b7639/fastani_result.tsv --threads 1
[2023-03-14 13:19:45,753] [INFO] Task succeeded: fastANI
[2023-03-14 13:19:45,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:19:45,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:19:45,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:19:45,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:19:45,754] [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
--------------------------------------------------------------------------------
[2023-03-14 13:19:45,754] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7639/tc_result.tsv
[2023-03-14 13:19:45,754] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:19:45,754] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:19:45,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/checkm_data
[2023-03-14 13:19:45,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:19:45,760] [INFO] Task started: CheckM
[2023-03-14 13:19:45,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7639/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7639/checkm_input OceanDNA-b7639/checkm_result
[2023-03-14 13:20:07,336] [INFO] Task succeeded: CheckM
[2023-03-14 13:20:07,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 13:20:07,340] [INFO] ===== Completeness check finished =====
[2023-03-14 13:20:07,340] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:20:07,341] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7639/markers.fasta)
[2023-03-14 13:20:07,341] [INFO] Task started: Blastn
[2023-03-14 13:20:07,342] [INFO] Running command: blastn -query OceanDNA-b7639/markers.fasta -db /var/lib/cwl/stgf5853613-76c5-475e-a2c9-532fa4ba962c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7639/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:20:08,134] [INFO] Task succeeded: Blastn
[2023-03-14 13:20:08,135] [INFO] Selected 23 target genomes.
[2023-03-14 13:20:08,136] [INFO] Target genome list was writen to OceanDNA-b7639/target_genomes_gtdb.txt
[2023-03-14 13:20:08,350] [INFO] Task started: fastANI
[2023-03-14 13:20:08,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ffa30f-ca48-4aad-b6c0-c1dbff086926/OceanDNA-b7639.fa --refList OceanDNA-b7639/target_genomes_gtdb.txt --output OceanDNA-b7639/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:20:18,592] [INFO] Task succeeded: fastANI
[2023-03-14 13:20:18,597] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:20:18,597] [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_902523635.1	s__MAG-121220-bin8 sp902523635	98.0183	168	252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002705485.1	s__MAG-121220-bin8 sp002705485	78.8691	115	252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.79	97.60	0.73	0.71	4	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	76.8269	59	252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	76.2711	51	252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	76.0411	53	252	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:20:18,598] [INFO] GTDB search result was written to OceanDNA-b7639/result_gtdb.tsv
[2023-03-14 13:20:18,598] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:20:18,599] [INFO] DFAST_QC result json was written to OceanDNA-b7639/dqc_result.json
[2023-03-14 13:20:18,599] [INFO] DFAST_QC completed!
[2023-03-14 13:20:18,599] [INFO] Total running time: 0h1m11s