[2023-03-15 15:51:29,967] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg9aaf1eb7-87c6-4c7a-890b-fb2e3c51dbb6/OceanDNA-b4624.fa | prodigal -d OceanDNA-b4624/cds.fna -a OceanDNA-b4624/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:49,300] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:49,300] [INFO] Task started: HMMsearch
[2023-03-15 15:51:49,300] [INFO] Running command: hmmsearch --tblout OceanDNA-b4624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/reference_markers.hmm OceanDNA-b4624/protein.faa > /dev/null
[2023-03-15 15:51:49,486] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:49,486] [INFO] Found 6/6 markers.
[2023-03-15 15:51:49,506] [INFO] Query marker FASTA was written to OceanDNA-b4624/markers.fasta
[2023-03-15 15:51:49,506] [INFO] Task started: Blastn
[2023-03-15 15:51:49,506] [INFO] Running command: blastn -query OceanDNA-b4624/markers.fasta -db /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/reference_markers.fasta -out OceanDNA-b4624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:50,080] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:50,080] [INFO] Selected 28 target genomes.
[2023-03-15 15:51:50,081] [INFO] Target genome list was writen to OceanDNA-b4624/target_genomes.txt
[2023-03-15 15:51:50,095] [INFO] Task started: fastANI
[2023-03-15 15:51:50,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaf1eb7-87c6-4c7a-890b-fb2e3c51dbb6/OceanDNA-b4624.fa --refList OceanDNA-b4624/target_genomes.txt --output OceanDNA-b4624/fastani_result.tsv --threads 1
[2023-03-15 15:52:05,380] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:05,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:52:05,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:52:05,380] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:52:05,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:52:05,380] [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
--------------------------------------------------------------------------------
[2023-03-15 15:52:05,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4624/tc_result.tsv
[2023-03-15 15:52:05,381] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:52:05,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:52:05,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/checkm_data
[2023-03-15 15:52:05,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:52:05,389] [INFO] Task started: CheckM
[2023-03-15 15:52:05,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4624/checkm_input OceanDNA-b4624/checkm_result
[2023-03-15 15:52:51,430] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:51,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:51,433] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:51,433] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:51,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4624/markers.fasta)
[2023-03-15 15:52:51,435] [INFO] Task started: Blastn
[2023-03-15 15:52:51,435] [INFO] Running command: blastn -query OceanDNA-b4624/markers.fasta -db /var/lib/cwl/stgd418141a-79b2-40d7-b76f-2ddffa25516b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:52,236] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:52,237] [INFO] Selected 32 target genomes.
[2023-03-15 15:52:52,237] [INFO] Target genome list was writen to OceanDNA-b4624/target_genomes_gtdb.txt
[2023-03-15 15:52:52,271] [INFO] Task started: fastANI
[2023-03-15 15:52:52,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaf1eb7-87c6-4c7a-890b-fb2e3c51dbb6/OceanDNA-b4624.fa --refList OceanDNA-b4624/target_genomes_gtdb.txt --output OceanDNA-b4624/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:53:07,262] [INFO] Task succeeded: fastANI
[2023-03-15 15:53:07,265] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:53:07,265] [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_002713215.1	s__UBA2108 sp002713215	77.4585	131	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA2108	95.0	99.97	99.97	0.98	0.98	2	-
GCA_002453255.1	s__UBA6770 sp002453255	77.2109	84	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA6770	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707155.1	s__UBA6770 sp002707155	77.1306	67	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__UBA6770	95.0	99.26	99.24	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 15:53:07,265] [INFO] GTDB search result was written to OceanDNA-b4624/result_gtdb.tsv
[2023-03-15 15:53:07,265] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:53:07,266] [INFO] DFAST_QC result json was written to OceanDNA-b4624/dqc_result.json
[2023-03-15 15:53:07,266] [INFO] DFAST_QC completed!
[2023-03-15 15:53:07,266] [INFO] Total running time: 0h1m37s