[2023-03-19 02:59:38,290] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference
[2023-03-19 02:59:39,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,387] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,387] [INFO] Running command: cat /var/lib/cwl/stgeb6d8138-197d-4ad8-bcb1-ce36456f2667/OceanDNA-b7440.fa | prodigal -d OceanDNA-b7440/cds.fna -a OceanDNA-b7440/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:49,557] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:49,557] [INFO] Task started: HMMsearch
[2023-03-19 02:59:49,557] [INFO] Running command: hmmsearch --tblout OceanDNA-b7440/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/reference_markers.hmm OceanDNA-b7440/protein.faa > /dev/null
[2023-03-19 02:59:49,711] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:49,711] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb6d8138-197d-4ad8-bcb1-ce36456f2667/OceanDNA-b7440.fa]
[2023-03-19 02:59:49,724] [INFO] Query marker FASTA was written to OceanDNA-b7440/markers.fasta
[2023-03-19 02:59:49,724] [INFO] Task started: Blastn
[2023-03-19 02:59:49,725] [INFO] Running command: blastn -query OceanDNA-b7440/markers.fasta -db /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/reference_markers.fasta -out OceanDNA-b7440/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:50,257] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:50,258] [INFO] Selected 24 target genomes.
[2023-03-19 02:59:50,258] [INFO] Target genome list was writen to OceanDNA-b7440/target_genomes.txt
[2023-03-19 02:59:50,267] [INFO] Task started: fastANI
[2023-03-19 02:59:50,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6d8138-197d-4ad8-bcb1-ce36456f2667/OceanDNA-b7440.fa --refList OceanDNA-b7440/target_genomes.txt --output OceanDNA-b7440/fastani_result.tsv --threads 1
[2023-03-19 03:00:03,363] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:03,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:00:03,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:00:03,368] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:00:03,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:00:03,368] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.129	57	494	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	75.9	59	494	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	75.8985	53	494	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	75.6752	51	494	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:00:03,369] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7440/tc_result.tsv
[2023-03-19 03:00:03,369] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:00:03,369] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:00:03,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/checkm_data
[2023-03-19 03:00:03,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:00:03,573] [INFO] Task started: CheckM
[2023-03-19 03:00:03,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7440/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7440/checkm_input OceanDNA-b7440/checkm_result
[2023-03-19 03:00:33,167] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:33,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:33,169] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:33,169] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:33,169] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7440/markers.fasta)
[2023-03-19 03:00:33,170] [INFO] Task started: Blastn
[2023-03-19 03:00:33,170] [INFO] Running command: blastn -query OceanDNA-b7440/markers.fasta -db /var/lib/cwl/stg42e83e47-9b3a-4adb-9f8c-660bec23b1cc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7440/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:33,887] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:33,888] [INFO] Selected 8 target genomes.
[2023-03-19 03:00:33,888] [INFO] Target genome list was writen to OceanDNA-b7440/target_genomes_gtdb.txt
[2023-03-19 03:00:33,896] [INFO] Task started: fastANI
[2023-03-19 03:00:33,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6d8138-197d-4ad8-bcb1-ce36456f2667/OceanDNA-b7440.fa --refList OceanDNA-b7440/target_genomes_gtdb.txt --output OceanDNA-b7440/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:36,891] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:36,896] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:00:36,897] [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_018608625.1	s__Hel1-33-131 sp018608625	86.5246	359	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	83.9242	317	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	81.0018	299	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	78.672	204	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	78.6073	240	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	78.4407	224	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	78.2462	197	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	77.9698	190	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:00:36,897] [INFO] GTDB search result was written to OceanDNA-b7440/result_gtdb.tsv
[2023-03-19 03:00:36,897] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:36,898] [INFO] DFAST_QC result json was written to OceanDNA-b7440/dqc_result.json
[2023-03-19 03:00:36,898] [INFO] DFAST_QC completed!
[2023-03-19 03:00:36,898] [INFO] Total running time: 0h0m59s