[2023-03-19 03:21:52,743] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:21:52,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:21:52,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference
[2023-03-19 03:21:53,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:21:53,862] [INFO] Task started: Prodigal
[2023-03-19 03:21:53,863] [INFO] Running command: cat /var/lib/cwl/stgbc62bb94-4fa6-4c60-aff6-49bae698a9c0/OceanDNA-b11919.fa | prodigal -d OceanDNA-b11919/cds.fna -a OceanDNA-b11919/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:22:12,712] [INFO] Task succeeded: Prodigal
[2023-03-19 03:22:12,713] [INFO] Task started: HMMsearch
[2023-03-19 03:22:12,713] [INFO] Running command: hmmsearch --tblout OceanDNA-b11919/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/reference_markers.hmm OceanDNA-b11919/protein.faa > /dev/null
[2023-03-19 03:22:12,915] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:22:12,915] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbc62bb94-4fa6-4c60-aff6-49bae698a9c0/OceanDNA-b11919.fa]
[2023-03-19 03:22:12,955] [INFO] Query marker FASTA was written to OceanDNA-b11919/markers.fasta
[2023-03-19 03:22:12,957] [INFO] Task started: Blastn
[2023-03-19 03:22:12,957] [INFO] Running command: blastn -query OceanDNA-b11919/markers.fasta -db /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/reference_markers.fasta -out OceanDNA-b11919/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:22:13,607] [INFO] Task succeeded: Blastn
[2023-03-19 03:22:13,614] [INFO] Selected 19 target genomes.
[2023-03-19 03:22:13,614] [INFO] Target genome list was writen to OceanDNA-b11919/target_genomes.txt
[2023-03-19 03:22:13,621] [INFO] Task started: fastANI
[2023-03-19 03:22:13,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc62bb94-4fa6-4c60-aff6-49bae698a9c0/OceanDNA-b11919.fa --refList OceanDNA-b11919/target_genomes.txt --output OceanDNA-b11919/fastani_result.tsv --threads 1
[2023-03-19 03:22:27,293] [INFO] Task succeeded: fastANI
[2023-03-19 03:22:27,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:22:27,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:22:27,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:22:27,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:22:27,294] [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
--------------------------------------------------------------------------------
[2023-03-19 03:22:27,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11919/tc_result.tsv
[2023-03-19 03:22:27,301] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:22:27,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:22:27,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/checkm_data
[2023-03-19 03:22:27,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:22:27,524] [INFO] Task started: CheckM
[2023-03-19 03:22:27,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11919/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11919/checkm_input OceanDNA-b11919/checkm_result
[2023-03-19 03:23:23,416] [INFO] Task succeeded: CheckM
[2023-03-19 03:23:23,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:23:23,540] [INFO] ===== Completeness check finished =====
[2023-03-19 03:23:23,540] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:23:23,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11919/markers.fasta)
[2023-03-19 03:23:23,542] [INFO] Task started: Blastn
[2023-03-19 03:23:23,542] [INFO] Running command: blastn -query OceanDNA-b11919/markers.fasta -db /var/lib/cwl/stg3e4f9a91-bbf0-427d-a345-c226f36fa435/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11919/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:24,550] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:24,574] [INFO] Selected 20 target genomes.
[2023-03-19 03:23:24,574] [INFO] Target genome list was writen to OceanDNA-b11919/target_genomes_gtdb.txt
[2023-03-19 03:23:24,628] [INFO] Task started: fastANI
[2023-03-19 03:23:24,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc62bb94-4fa6-4c60-aff6-49bae698a9c0/OceanDNA-b11919.fa --refList OceanDNA-b11919/target_genomes_gtdb.txt --output OceanDNA-b11919/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:23:34,337] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:34,341] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:23:34,341] [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_002313415.1	s__UBA11663 sp002313415	99.5653	541	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	99.13	99.10	0.82	0.81	3	conclusive
GCA_002863145.1	s__UBA11663 sp002863145	78.6721	264	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_002683345.1	s__UBA11663 sp002683345	77.9516	211	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524845.1	s__UBA11663 sp011524845	77.4852	135	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469765.1	s__UBA11663 sp002469765	76.9609	98	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729115.1	s__UBA11663 sp002729115	76.8555	93	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
--------------------------------------------------------------------------------
[2023-03-19 03:23:34,344] [INFO] GTDB search result was written to OceanDNA-b11919/result_gtdb.tsv
[2023-03-19 03:23:34,346] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:23:34,350] [INFO] DFAST_QC result json was written to OceanDNA-b11919/dqc_result.json
[2023-03-19 03:23:34,350] [INFO] DFAST_QC completed!
[2023-03-19 03:23:34,350] [INFO] Total running time: 0h1m42s