[2023-03-17 06:30:51,154] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:51,154] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:51,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference
[2023-03-17 06:30:52,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:52,377] [INFO] Task started: Prodigal
[2023-03-17 06:30:52,377] [INFO] Running command: cat /var/lib/cwl/stg200ed3ce-ce6f-4dc6-96c8-0ef2b829e993/OceanDNA-b11822.fa | prodigal -d OceanDNA-b11822/cds.fna -a OceanDNA-b11822/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:10,604] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:10,605] [INFO] Task started: HMMsearch
[2023-03-17 06:31:10,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b11822/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/reference_markers.hmm OceanDNA-b11822/protein.faa > /dev/null
[2023-03-17 06:31:10,789] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:10,791] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg200ed3ce-ce6f-4dc6-96c8-0ef2b829e993/OceanDNA-b11822.fa]
[2023-03-17 06:31:10,807] [INFO] Query marker FASTA was written to OceanDNA-b11822/markers.fasta
[2023-03-17 06:31:10,807] [INFO] Task started: Blastn
[2023-03-17 06:31:10,807] [INFO] Running command: blastn -query OceanDNA-b11822/markers.fasta -db /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/reference_markers.fasta -out OceanDNA-b11822/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:11,334] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:11,335] [INFO] Selected 19 target genomes.
[2023-03-17 06:31:11,335] [INFO] Target genome list was writen to OceanDNA-b11822/target_genomes.txt
[2023-03-17 06:31:11,346] [INFO] Task started: fastANI
[2023-03-17 06:31:11,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg200ed3ce-ce6f-4dc6-96c8-0ef2b829e993/OceanDNA-b11822.fa --refList OceanDNA-b11822/target_genomes.txt --output OceanDNA-b11822/fastani_result.tsv --threads 1
[2023-03-17 06:31:24,331] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:24,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:24,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:24,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:24,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:24,332] [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
--------------------------------------------------------------------------------
[2023-03-17 06:31:24,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11822/tc_result.tsv
[2023-03-17 06:31:24,332] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:24,332] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:24,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/checkm_data
[2023-03-17 06:31:24,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:24,338] [INFO] Task started: CheckM
[2023-03-17 06:31:24,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11822/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11822/checkm_input OceanDNA-b11822/checkm_result
[2023-03-17 06:32:13,129] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:13,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:13,131] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:13,131] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:13,132] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11822/markers.fasta)
[2023-03-17 06:32:13,132] [INFO] Task started: Blastn
[2023-03-17 06:32:13,132] [INFO] Running command: blastn -query OceanDNA-b11822/markers.fasta -db /var/lib/cwl/stg72f92d5b-3600-418b-a140-86cd0c9b6afe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11822/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:13,880] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:13,881] [INFO] Selected 17 target genomes.
[2023-03-17 06:32:13,881] [INFO] Target genome list was writen to OceanDNA-b11822/target_genomes_gtdb.txt
[2023-03-17 06:32:14,248] [INFO] Task started: fastANI
[2023-03-17 06:32:14,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg200ed3ce-ce6f-4dc6-96c8-0ef2b829e993/OceanDNA-b11822.fa --refList OceanDNA-b11822/target_genomes_gtdb.txt --output OceanDNA-b11822/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:20,940] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:20,943] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:32:20,943] [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_002690915.1	s__UA16 sp002690915	97.09	554	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	96.97	96.97	0.71	0.71	2	conclusive
GCA_002863125.1	s__UA16 sp002863125	80.7042	447	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
GCA_002448555.1	s__UA16 sp002448555	80.3031	379	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.35	99.35	0.96	0.96	2	-
GCA_002420235.1	s__UA16 sp002420235	78.636	289	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.27	97.82	0.87	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:20,944] [INFO] GTDB search result was written to OceanDNA-b11822/result_gtdb.tsv
[2023-03-17 06:32:20,944] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:20,944] [INFO] DFAST_QC result json was written to OceanDNA-b11822/dqc_result.json
[2023-03-17 06:32:20,944] [INFO] DFAST_QC completed!
[2023-03-17 06:32:20,944] [INFO] Total running time: 0h1m30s