[2023-03-17 05:26:45,821] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,821] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference
[2023-03-17 05:26:46,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,920] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,920] [INFO] Running command: cat /var/lib/cwl/stga6da427f-4026-4776-94b8-c25feb6226c3/OceanDNA-b11083.fa | prodigal -d OceanDNA-b11083/cds.fna -a OceanDNA-b11083/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:26:52,227] [INFO] Task succeeded: Prodigal
[2023-03-17 05:26:52,227] [INFO] Task started: HMMsearch
[2023-03-17 05:26:52,227] [INFO] Running command: hmmsearch --tblout OceanDNA-b11083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/reference_markers.hmm OceanDNA-b11083/protein.faa > /dev/null
[2023-03-17 05:26:52,377] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:26:52,377] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga6da427f-4026-4776-94b8-c25feb6226c3/OceanDNA-b11083.fa]
[2023-03-17 05:26:52,386] [INFO] Query marker FASTA was written to OceanDNA-b11083/markers.fasta
[2023-03-17 05:26:52,387] [INFO] Task started: Blastn
[2023-03-17 05:26:52,387] [INFO] Running command: blastn -query OceanDNA-b11083/markers.fasta -db /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/reference_markers.fasta -out OceanDNA-b11083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:26:52,914] [INFO] Task succeeded: Blastn
[2023-03-17 05:26:52,915] [INFO] Selected 28 target genomes.
[2023-03-17 05:26:52,915] [INFO] Target genome list was writen to OceanDNA-b11083/target_genomes.txt
[2023-03-17 05:26:52,931] [INFO] Task started: fastANI
[2023-03-17 05:26:52,932] [INFO] Running command: fastANI --query /var/lib/cwl/stga6da427f-4026-4776-94b8-c25feb6226c3/OceanDNA-b11083.fa --refList OceanDNA-b11083/target_genomes.txt --output OceanDNA-b11083/fastani_result.tsv --threads 1
[2023-03-17 05:27:07,682] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:07,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:07,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:07,683] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:07,683] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:27:07,683] [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
--------------------------------------------------------------------------------
[2023-03-17 05:27:07,683] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11083/tc_result.tsv
[2023-03-17 05:27:07,683] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:07,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:07,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/checkm_data
[2023-03-17 05:27:07,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:07,688] [INFO] Task started: CheckM
[2023-03-17 05:27:07,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11083/checkm_input OceanDNA-b11083/checkm_result
[2023-03-17 05:27:26,880] [INFO] Task succeeded: CheckM
[2023-03-17 05:27:26,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:27:26,882] [INFO] ===== Completeness check finished =====
[2023-03-17 05:27:26,882] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:27:26,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11083/markers.fasta)
[2023-03-17 05:27:26,883] [INFO] Task started: Blastn
[2023-03-17 05:27:26,883] [INFO] Running command: blastn -query OceanDNA-b11083/markers.fasta -db /var/lib/cwl/stg5ab38c69-4f25-4570-b51b-f82e14b1c467/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:27,639] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:27,640] [INFO] Selected 12 target genomes.
[2023-03-17 05:27:27,640] [INFO] Target genome list was writen to OceanDNA-b11083/target_genomes_gtdb.txt
[2023-03-17 05:27:27,882] [INFO] Task started: fastANI
[2023-03-17 05:27:27,882] [INFO] Running command: fastANI --query /var/lib/cwl/stga6da427f-4026-4776-94b8-c25feb6226c3/OceanDNA-b11083.fa --refList OceanDNA-b11083/target_genomes_gtdb.txt --output OceanDNA-b11083/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:27:31,655] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:31,659] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:27:31,659] [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_017856205.1	s__UBA7446 sp017856205	77.6691	75	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331305.1	s__UBA7446 sp002470745	77.3643	64	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.36	99.14	0.86	0.83	3	-
GCA_002478685.1	s__UBA7446 sp002478685	77.3399	68	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
GCA_009937085.1	s__UBA7446 sp009937085	77.2588	75	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:27:31,659] [INFO] GTDB search result was written to OceanDNA-b11083/result_gtdb.tsv
[2023-03-17 05:27:31,659] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:27:31,660] [INFO] DFAST_QC result json was written to OceanDNA-b11083/dqc_result.json
[2023-03-17 05:27:31,660] [INFO] DFAST_QC completed!
[2023-03-17 05:27:31,660] [INFO] Total running time: 0h0m46s