[2023-03-14 11:13:58,986] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,987] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference
[2023-03-14 11:14:00,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stg942fb011-bc1f-4d22-96cc-54f15fab9e69/OceanDNA-b4976.fa | prodigal -d OceanDNA-b4976/cds.fna -a OceanDNA-b4976/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:06,772] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:06,772] [INFO] Task started: HMMsearch
[2023-03-14 11:14:06,772] [INFO] Running command: hmmsearch --tblout OceanDNA-b4976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/reference_markers.hmm OceanDNA-b4976/protein.faa > /dev/null
[2023-03-14 11:14:06,936] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:06,936] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg942fb011-bc1f-4d22-96cc-54f15fab9e69/OceanDNA-b4976.fa]
[2023-03-14 11:14:06,945] [INFO] Query marker FASTA was written to OceanDNA-b4976/markers.fasta
[2023-03-14 11:14:06,946] [INFO] Task started: Blastn
[2023-03-14 11:14:06,946] [INFO] Running command: blastn -query OceanDNA-b4976/markers.fasta -db /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/reference_markers.fasta -out OceanDNA-b4976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:07,509] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:07,510] [INFO] Selected 23 target genomes.
[2023-03-14 11:14:07,510] [INFO] Target genome list was writen to OceanDNA-b4976/target_genomes.txt
[2023-03-14 11:14:07,526] [INFO] Task started: fastANI
[2023-03-14 11:14:07,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg942fb011-bc1f-4d22-96cc-54f15fab9e69/OceanDNA-b4976.fa --refList OceanDNA-b4976/target_genomes.txt --output OceanDNA-b4976/fastani_result.tsv --threads 1
[2023-03-14 11:14:20,934] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:20,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:20,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:20,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:20,935] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:20,935] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:20,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4976/tc_result.tsv
[2023-03-14 11:14:20,935] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:20,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:20,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/checkm_data
[2023-03-14 11:14:20,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:20,942] [INFO] Task started: CheckM
[2023-03-14 11:14:20,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4976/checkm_input OceanDNA-b4976/checkm_result
[2023-03-14 11:14:42,252] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:42,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:42,254] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:42,254] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:42,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4976/markers.fasta)
[2023-03-14 11:14:42,255] [INFO] Task started: Blastn
[2023-03-14 11:14:42,256] [INFO] Running command: blastn -query OceanDNA-b4976/markers.fasta -db /var/lib/cwl/stg5a1cfa74-70c4-4aca-9bc9-371ac08c5611/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:43,223] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:43,224] [INFO] Selected 18 target genomes.
[2023-03-14 11:14:43,224] [INFO] Target genome list was writen to OceanDNA-b4976/target_genomes_gtdb.txt
[2023-03-14 11:14:43,244] [INFO] Task started: fastANI
[2023-03-14 11:14:43,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg942fb011-bc1f-4d22-96cc-54f15fab9e69/OceanDNA-b4976.fa --refList OceanDNA-b4976/target_genomes_gtdb.txt --output OceanDNA-b4976/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:50,583] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:50,588] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:14:50,588] [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	87.9622	157	345	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	77.9839	147	345	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	77.7683	106	345	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	77.5247	117	345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	77.4096	111	345	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_002728175.1	s__GCA-2697505 sp002728175	76.3495	60	345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	76.1875	66	345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-14 11:14:50,589] [INFO] GTDB search result was written to OceanDNA-b4976/result_gtdb.tsv
[2023-03-14 11:14:50,589] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:50,589] [INFO] DFAST_QC result json was written to OceanDNA-b4976/dqc_result.json
[2023-03-14 11:14:50,589] [INFO] DFAST_QC completed!
[2023-03-14 11:14:50,590] [INFO] Total running time: 0h0m52s