[2023-03-17 02:57:51,829] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:57:51,830] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:57:51,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference
[2023-03-17 02:57:53,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:57:53,077] [INFO] Task started: Prodigal
[2023-03-17 02:57:53,078] [INFO] Running command: cat /var/lib/cwl/stg72a3fe01-30c1-49c9-946d-7283c6abac01/OceanDNA-b8670.fa | prodigal -d OceanDNA-b8670/cds.fna -a OceanDNA-b8670/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:57:58,381] [INFO] Task succeeded: Prodigal
[2023-03-17 02:57:58,381] [INFO] Task started: HMMsearch
[2023-03-17 02:57:58,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b8670/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/reference_markers.hmm OceanDNA-b8670/protein.faa > /dev/null
[2023-03-17 02:57:58,614] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:57:58,615] [INFO] Found 6/6 markers.
[2023-03-17 02:57:58,630] [INFO] Query marker FASTA was written to OceanDNA-b8670/markers.fasta
[2023-03-17 02:57:58,632] [INFO] Task started: Blastn
[2023-03-17 02:57:58,632] [INFO] Running command: blastn -query OceanDNA-b8670/markers.fasta -db /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/reference_markers.fasta -out OceanDNA-b8670/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:57:59,531] [INFO] Task succeeded: Blastn
[2023-03-17 02:57:59,541] [INFO] Selected 33 target genomes.
[2023-03-17 02:57:59,541] [INFO] Target genome list was writen to OceanDNA-b8670/target_genomes.txt
[2023-03-17 02:57:59,561] [INFO] Task started: fastANI
[2023-03-17 02:57:59,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a3fe01-30c1-49c9-946d-7283c6abac01/OceanDNA-b8670.fa --refList OceanDNA-b8670/target_genomes.txt --output OceanDNA-b8670/fastani_result.tsv --threads 1
[2023-03-17 02:58:19,023] [INFO] Task succeeded: fastANI
[2023-03-17 02:58:19,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:58:19,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:58:19,024] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:58:19,024] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:58:19,024] [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 02:58:19,024] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8670/tc_result.tsv
[2023-03-17 02:58:19,024] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:58:19,025] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:58:19,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/checkm_data
[2023-03-17 02:58:19,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:58:19,037] [INFO] Task started: CheckM
[2023-03-17 02:58:19,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8670/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8670/checkm_input OceanDNA-b8670/checkm_result
[2023-03-17 02:58:40,317] [INFO] Task succeeded: CheckM
[2023-03-17 02:58:40,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:58:40,369] [INFO] ===== Completeness check finished =====
[2023-03-17 02:58:40,369] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:58:40,369] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8670/markers.fasta)
[2023-03-17 02:58:40,371] [INFO] Task started: Blastn
[2023-03-17 02:58:40,371] [INFO] Running command: blastn -query OceanDNA-b8670/markers.fasta -db /var/lib/cwl/stg4342b64c-d625-4506-8fea-21e608d38499/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8670/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:58:41,345] [INFO] Task succeeded: Blastn
[2023-03-17 02:58:41,355] [INFO] Selected 15 target genomes.
[2023-03-17 02:58:41,355] [INFO] Target genome list was writen to OceanDNA-b8670/target_genomes_gtdb.txt
[2023-03-17 02:58:41,565] [INFO] Task started: fastANI
[2023-03-17 02:58:41,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a3fe01-30c1-49c9-946d-7283c6abac01/OceanDNA-b8670.fa --refList OceanDNA-b8670/target_genomes_gtdb.txt --output OceanDNA-b8670/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:58:45,265] [INFO] Task succeeded: fastANI
[2023-03-17 02:58:45,272] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:58:45,272] [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_902602415.1	s__MED-G13 sp902602415	98.1385	206	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.01	98.13	0.87	0.81	5	conclusive
GCA_902525795.1	s__MED-G13 sp902525795	89.6059	183	247	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_002457735.1	s__MED-G13 sp002457735	87.748	183	247	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_902518355.1	s__MED-G13 sp902518355	77.4825	73	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902510415.1	s__MED-G13 sp902510415	77.4763	62	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902604715.1	s__MED-G13 sp902604715	77.2132	62	247	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_902519075.1	s__MED-G13 sp902519075	77.1712	62	247	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_902557655.1	s__MED-G13 sp902557655	77.0571	76	247	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_002697255.1	s__MED-G13 sp002697255	76.9324	73	247	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_902510475.1	s__MED-G13 sp902510475	76.9188	59	247	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_902608795.1	s__MED-G13 sp902608795	76.8716	59	247	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 02:58:45,276] [INFO] GTDB search result was written to OceanDNA-b8670/result_gtdb.tsv
[2023-03-17 02:58:45,276] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:58:45,281] [INFO] DFAST_QC result json was written to OceanDNA-b8670/dqc_result.json
[2023-03-17 02:58:45,281] [INFO] DFAST_QC completed!
[2023-03-17 02:58:45,281] [INFO] Total running time: 0h0m53s