[2023-03-15 07:49:00,149] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:49:00,151] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:49:00,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference
[2023-03-15 07:49:01,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:49:01,278] [INFO] Task started: Prodigal
[2023-03-15 07:49:01,278] [INFO] Running command: cat /var/lib/cwl/stg84f18cca-d0bd-431d-bc20-58150264a17c/OceanDNA-b4988.fa | prodigal -d OceanDNA-b4988/cds.fna -a OceanDNA-b4988/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:49:06,103] [INFO] Task succeeded: Prodigal
[2023-03-15 07:49:06,103] [INFO] Task started: HMMsearch
[2023-03-15 07:49:06,103] [INFO] Running command: hmmsearch --tblout OceanDNA-b4988/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/reference_markers.hmm OceanDNA-b4988/protein.faa > /dev/null
[2023-03-15 07:49:06,289] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:49:06,289] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg84f18cca-d0bd-431d-bc20-58150264a17c/OceanDNA-b4988.fa]
[2023-03-15 07:49:06,309] [INFO] Query marker FASTA was written to OceanDNA-b4988/markers.fasta
[2023-03-15 07:49:06,309] [INFO] Task started: Blastn
[2023-03-15 07:49:06,309] [INFO] Running command: blastn -query OceanDNA-b4988/markers.fasta -db /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/reference_markers.fasta -out OceanDNA-b4988/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:06,863] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:06,885] [INFO] Selected 26 target genomes.
[2023-03-15 07:49:06,886] [INFO] Target genome list was writen to OceanDNA-b4988/target_genomes.txt
[2023-03-15 07:49:06,899] [INFO] Task started: fastANI
[2023-03-15 07:49:06,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f18cca-d0bd-431d-bc20-58150264a17c/OceanDNA-b4988.fa --refList OceanDNA-b4988/target_genomes.txt --output OceanDNA-b4988/fastani_result.tsv --threads 1
[2023-03-15 07:49:21,571] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:21,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:49:21,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:49:21,572] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:49:21,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:49:21,572] [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 07:49:21,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4988/tc_result.tsv
[2023-03-15 07:49:21,574] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:49:21,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:49:21,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/checkm_data
[2023-03-15 07:49:21,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:49:21,593] [INFO] Task started: CheckM
[2023-03-15 07:49:21,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4988/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4988/checkm_input OceanDNA-b4988/checkm_result
[2023-03-15 07:49:39,967] [INFO] Task succeeded: CheckM
[2023-03-15 07:49:39,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:49:40,032] [INFO] ===== Completeness check finished =====
[2023-03-15 07:49:40,032] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:49:40,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4988/markers.fasta)
[2023-03-15 07:49:40,033] [INFO] Task started: Blastn
[2023-03-15 07:49:40,033] [INFO] Running command: blastn -query OceanDNA-b4988/markers.fasta -db /var/lib/cwl/stg06538b74-4a84-412e-a233-205bcc7222cc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4988/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:40,913] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:40,922] [INFO] Selected 22 target genomes.
[2023-03-15 07:49:40,923] [INFO] Target genome list was writen to OceanDNA-b4988/target_genomes_gtdb.txt
[2023-03-15 07:49:40,947] [INFO] Task started: fastANI
[2023-03-15 07:49:40,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f18cca-d0bd-431d-bc20-58150264a17c/OceanDNA-b4988.fa --refList OceanDNA-b4988/target_genomes_gtdb.txt --output OceanDNA-b4988/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:49:48,014] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:48,018] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:49:48,018] [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_002689735.1	s__GCA-002715885 sp002689735	91.0074	125	256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_014239655.1	s__GCA-002715885 sp014239655	78.2671	91	256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	78.0962	80	256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	77.954	83	256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181585.1	s__CAJIYG01 sp905181585	77.6817	82	256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:49:48,020] [INFO] GTDB search result was written to OceanDNA-b4988/result_gtdb.tsv
[2023-03-15 07:49:48,021] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:49:48,023] [INFO] DFAST_QC result json was written to OceanDNA-b4988/dqc_result.json
[2023-03-15 07:49:48,024] [INFO] DFAST_QC completed!
[2023-03-15 07:49:48,024] [INFO] Total running time: 0h0m48s