[2023-03-16 07:15:38,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:15:38,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:15:38,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference
[2023-03-16 07:15:40,006] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:15:40,006] [INFO] Task started: Prodigal
[2023-03-16 07:15:40,006] [INFO] Running command: cat /var/lib/cwl/stgf3132d67-a941-48ca-87a4-4234c665dfaf/OceanDNA-b3597.fa | prodigal -d OceanDNA-b3597/cds.fna -a OceanDNA-b3597/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:15:50,966] [INFO] Task succeeded: Prodigal
[2023-03-16 07:15:50,966] [INFO] Task started: HMMsearch
[2023-03-16 07:15:50,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b3597/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/reference_markers.hmm OceanDNA-b3597/protein.faa > /dev/null
[2023-03-16 07:15:51,145] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:15:51,146] [INFO] Found 6/6 markers.
[2023-03-16 07:15:51,158] [INFO] Query marker FASTA was written to OceanDNA-b3597/markers.fasta
[2023-03-16 07:15:51,159] [INFO] Task started: Blastn
[2023-03-16 07:15:51,159] [INFO] Running command: blastn -query OceanDNA-b3597/markers.fasta -db /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/reference_markers.fasta -out OceanDNA-b3597/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:15:51,735] [INFO] Task succeeded: Blastn
[2023-03-16 07:15:51,792] [INFO] Selected 26 target genomes.
[2023-03-16 07:15:51,792] [INFO] Target genome list was writen to OceanDNA-b3597/target_genomes.txt
[2023-03-16 07:15:51,810] [INFO] Task started: fastANI
[2023-03-16 07:15:51,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3132d67-a941-48ca-87a4-4234c665dfaf/OceanDNA-b3597.fa --refList OceanDNA-b3597/target_genomes.txt --output OceanDNA-b3597/fastani_result.tsv --threads 1
[2023-03-16 07:16:14,353] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:14,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:16:14,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:16:14,354] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:16:14,354] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:16:14,354] [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
--------------------------------------------------------------------------------
[2023-03-16 07:16:14,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3597/tc_result.tsv
[2023-03-16 07:16:14,355] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:16:14,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:16:14,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/checkm_data
[2023-03-16 07:16:14,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:16:14,361] [INFO] Task started: CheckM
[2023-03-16 07:16:14,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3597/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3597/checkm_input OceanDNA-b3597/checkm_result
[2023-03-16 07:16:46,098] [INFO] Task succeeded: CheckM
[2023-03-16 07:16:46,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.90%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:16:46,100] [INFO] ===== Completeness check finished =====
[2023-03-16 07:16:46,100] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:16:46,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3597/markers.fasta)
[2023-03-16 07:16:46,102] [INFO] Task started: Blastn
[2023-03-16 07:16:46,102] [INFO] Running command: blastn -query OceanDNA-b3597/markers.fasta -db /var/lib/cwl/stg2bcaaa2b-71c0-427d-b23f-be88eca0e7e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3597/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:16:47,054] [INFO] Task succeeded: Blastn
[2023-03-16 07:16:47,055] [INFO] Selected 20 target genomes.
[2023-03-16 07:16:47,056] [INFO] Target genome list was writen to OceanDNA-b3597/target_genomes_gtdb.txt
[2023-03-16 07:16:47,104] [INFO] Task started: fastANI
[2023-03-16 07:16:47,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3132d67-a941-48ca-87a4-4234c665dfaf/OceanDNA-b3597.fa --refList OceanDNA-b3597/target_genomes_gtdb.txt --output OceanDNA-b3597/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:16:58,716] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:58,719] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:16:58,719] [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_003489485.1	s__JJ008 sp003489485	96.3152	293	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.38	96.92	0.79	0.76	3	conclusive
GCA_016872155.1	s__JJ008 sp016872155	79.8461	262	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872195.1	s__JJ008 sp016872195	78.6259	229	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342205.1	s__JJ008 sp002342205	76.4126	54	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.68	98.09	0.85	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-16 07:16:58,720] [INFO] GTDB search result was written to OceanDNA-b3597/result_gtdb.tsv
[2023-03-16 07:16:58,720] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:16:58,721] [INFO] DFAST_QC result json was written to OceanDNA-b3597/dqc_result.json
[2023-03-16 07:16:58,721] [INFO] DFAST_QC completed!
[2023-03-16 07:16:58,721] [INFO] Total running time: 0h1m20s