[2023-03-17 08:56:41,466] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:56:41,466] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:56:41,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference
[2023-03-17 08:56:42,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:56:42,676] [INFO] Task started: Prodigal
[2023-03-17 08:56:42,677] [INFO] Running command: cat /var/lib/cwl/stgbe3e8b3b-2b58-41a0-ab22-3e5e1974915a/OceanDNA-b8672.fa | prodigal -d OceanDNA-b8672/cds.fna -a OceanDNA-b8672/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:56:48,107] [INFO] Task succeeded: Prodigal
[2023-03-17 08:56:48,108] [INFO] Task started: HMMsearch
[2023-03-17 08:56:48,108] [INFO] Running command: hmmsearch --tblout OceanDNA-b8672/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/reference_markers.hmm OceanDNA-b8672/protein.faa > /dev/null
[2023-03-17 08:56:48,257] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:56:48,258] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbe3e8b3b-2b58-41a0-ab22-3e5e1974915a/OceanDNA-b8672.fa]
[2023-03-17 08:56:48,266] [INFO] Query marker FASTA was written to OceanDNA-b8672/markers.fasta
[2023-03-17 08:56:48,267] [INFO] Task started: Blastn
[2023-03-17 08:56:48,267] [INFO] Running command: blastn -query OceanDNA-b8672/markers.fasta -db /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/reference_markers.fasta -out OceanDNA-b8672/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:56:48,903] [INFO] Task succeeded: Blastn
[2023-03-17 08:56:48,904] [INFO] Selected 23 target genomes.
[2023-03-17 08:56:48,904] [INFO] Target genome list was writen to OceanDNA-b8672/target_genomes.txt
[2023-03-17 08:56:49,253] [INFO] Task started: fastANI
[2023-03-17 08:56:49,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe3e8b3b-2b58-41a0-ab22-3e5e1974915a/OceanDNA-b8672.fa --refList OceanDNA-b8672/target_genomes.txt --output OceanDNA-b8672/fastani_result.tsv --threads 1
[2023-03-17 08:57:02,439] [INFO] Task succeeded: fastANI
[2023-03-17 08:57:02,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:57:02,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:57:02,439] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:57:02,439] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:57:02,439] [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 08:57:02,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8672/tc_result.tsv
[2023-03-17 08:57:02,440] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:57:02,440] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:57:02,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/checkm_data
[2023-03-17 08:57:02,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:57:02,562] [INFO] Task started: CheckM
[2023-03-17 08:57:02,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8672/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8672/checkm_input OceanDNA-b8672/checkm_result
[2023-03-17 08:57:23,716] [INFO] Task succeeded: CheckM
[2023-03-17 08:57:23,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.10%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:57:23,717] [INFO] ===== Completeness check finished =====
[2023-03-17 08:57:23,718] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:57:23,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8672/markers.fasta)
[2023-03-17 08:57:23,719] [INFO] Task started: Blastn
[2023-03-17 08:57:23,719] [INFO] Running command: blastn -query OceanDNA-b8672/markers.fasta -db /var/lib/cwl/stg3a9fba5c-dace-4290-8c0e-541e6dda829a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8672/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:57:24,904] [INFO] Task succeeded: Blastn
[2023-03-17 08:57:24,905] [INFO] Selected 12 target genomes.
[2023-03-17 08:57:24,905] [INFO] Target genome list was writen to OceanDNA-b8672/target_genomes_gtdb.txt
[2023-03-17 08:57:25,090] [INFO] Task started: fastANI
[2023-03-17 08:57:25,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe3e8b3b-2b58-41a0-ab22-3e5e1974915a/OceanDNA-b8672.fa --refList OceanDNA-b8672/target_genomes_gtdb.txt --output OceanDNA-b8672/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:57:27,618] [INFO] Task succeeded: fastANI
[2023-03-17 08:57:27,624] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:57:27,624] [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_902525795.1	s__MED-G13 sp902525795	95.4137	198	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902602415.1	s__MED-G13 sp902602415	89.9967	223	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.01	98.13	0.87	0.81	5	-
GCA_002457735.1	s__MED-G13 sp002457735	88.1523	199	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604715.1	s__MED-G13 sp902604715	77.6222	66	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902560045.1	s__MED-G13 sp902560045	77.228	56	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_902557655.1	s__MED-G13 sp902557655	76.919	68	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902510475.1	s__MED-G13 sp902510475	76.7662	63	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626585.1	s__MED-G13 sp902626585	76.7295	62	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.3313	79	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:57:27,624] [INFO] GTDB search result was written to OceanDNA-b8672/result_gtdb.tsv
[2023-03-17 08:57:27,624] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:57:27,625] [INFO] DFAST_QC result json was written to OceanDNA-b8672/dqc_result.json
[2023-03-17 08:57:27,625] [INFO] DFAST_QC completed!
[2023-03-17 08:57:27,625] [INFO] Total running time: 0h0m46s