[2023-03-18 04:39:10,676] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:10,676] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:10,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference
[2023-03-18 04:39:11,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:11,777] [INFO] Task started: Prodigal
[2023-03-18 04:39:11,777] [INFO] Running command: cat /var/lib/cwl/stg2f7540d0-7898-444a-b32c-2e9afd2198f4/OceanDNA-b5723.fa | prodigal -d OceanDNA-b5723/cds.fna -a OceanDNA-b5723/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:21,129] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:21,130] [INFO] Task started: HMMsearch
[2023-03-18 04:39:21,130] [INFO] Running command: hmmsearch --tblout OceanDNA-b5723/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/reference_markers.hmm OceanDNA-b5723/protein.faa > /dev/null
[2023-03-18 04:39:21,287] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:21,287] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f7540d0-7898-444a-b32c-2e9afd2198f4/OceanDNA-b5723.fa]
[2023-03-18 04:39:21,298] [INFO] Query marker FASTA was written to OceanDNA-b5723/markers.fasta
[2023-03-18 04:39:21,298] [INFO] Task started: Blastn
[2023-03-18 04:39:21,298] [INFO] Running command: blastn -query OceanDNA-b5723/markers.fasta -db /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/reference_markers.fasta -out OceanDNA-b5723/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:21,830] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:21,831] [INFO] Selected 24 target genomes.
[2023-03-18 04:39:21,831] [INFO] Target genome list was writen to OceanDNA-b5723/target_genomes.txt
[2023-03-18 04:39:21,840] [INFO] Task started: fastANI
[2023-03-18 04:39:21,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f7540d0-7898-444a-b32c-2e9afd2198f4/OceanDNA-b5723.fa --refList OceanDNA-b5723/target_genomes.txt --output OceanDNA-b5723/fastani_result.tsv --threads 1
[2023-03-18 04:39:33,958] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:33,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:39:33,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:39:33,959] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:39:33,959] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:39:33,959] [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
--------------------------------------------------------------------------------
[2023-03-18 04:39:33,959] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5723/tc_result.tsv
[2023-03-18 04:39:33,959] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:39:33,959] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:39:33,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/checkm_data
[2023-03-18 04:39:33,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:39:34,090] [INFO] Task started: CheckM
[2023-03-18 04:39:34,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5723/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5723/checkm_input OceanDNA-b5723/checkm_result
[2023-03-18 04:40:02,935] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:02,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:02,937] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:02,937] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:02,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5723/markers.fasta)
[2023-03-18 04:40:02,939] [INFO] Task started: Blastn
[2023-03-18 04:40:02,939] [INFO] Running command: blastn -query OceanDNA-b5723/markers.fasta -db /var/lib/cwl/stg3f5ec51d-d4d9-4e61-89da-a016039778fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5723/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:03,640] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:03,640] [INFO] Selected 20 target genomes.
[2023-03-18 04:40:03,641] [INFO] Target genome list was writen to OceanDNA-b5723/target_genomes_gtdb.txt
[2023-03-18 04:40:03,674] [INFO] Task started: fastANI
[2023-03-18 04:40:03,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f7540d0-7898-444a-b32c-2e9afd2198f4/OceanDNA-b5723.fa --refList OceanDNA-b5723/target_genomes_gtdb.txt --output OceanDNA-b5723/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:40:11,577] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:11,579] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:40:11,580] [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_002682945.1	s__TMED14 sp002682945	99.4616	432	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167805.1	s__TMED14 sp002167805	94.0056	432	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	95.87	95.87	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 04:40:11,580] [INFO] GTDB search result was written to OceanDNA-b5723/result_gtdb.tsv
[2023-03-18 04:40:11,580] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:40:11,580] [INFO] DFAST_QC result json was written to OceanDNA-b5723/dqc_result.json
[2023-03-18 04:40:11,580] [INFO] DFAST_QC completed!
[2023-03-18 04:40:11,580] [INFO] Total running time: 0h1m1s