[2023-03-14 14:06:09,275] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:06:09,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:06:09,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference
[2023-03-14 14:06:10,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:06:10,397] [INFO] Task started: Prodigal
[2023-03-14 14:06:10,397] [INFO] Running command: cat /var/lib/cwl/stgefb5a42c-0ed2-4ffa-b8df-2eccea7c267e/OceanDNA-b34721.fa | prodigal -d OceanDNA-b34721/cds.fna -a OceanDNA-b34721/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:06:36,724] [INFO] Task succeeded: Prodigal
[2023-03-14 14:06:36,724] [INFO] Task started: HMMsearch
[2023-03-14 14:06:36,724] [INFO] Running command: hmmsearch --tblout OceanDNA-b34721/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/reference_markers.hmm OceanDNA-b34721/protein.faa > /dev/null
[2023-03-14 14:06:36,947] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:06:36,947] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgefb5a42c-0ed2-4ffa-b8df-2eccea7c267e/OceanDNA-b34721.fa]
[2023-03-14 14:06:36,972] [INFO] Query marker FASTA was written to OceanDNA-b34721/markers.fasta
[2023-03-14 14:06:36,973] [INFO] Task started: Blastn
[2023-03-14 14:06:36,973] [INFO] Running command: blastn -query OceanDNA-b34721/markers.fasta -db /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/reference_markers.fasta -out OceanDNA-b34721/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:06:37,585] [INFO] Task succeeded: Blastn
[2023-03-14 14:06:37,586] [INFO] Selected 18 target genomes.
[2023-03-14 14:06:37,586] [INFO] Target genome list was writen to OceanDNA-b34721/target_genomes.txt
[2023-03-14 14:06:37,593] [INFO] Task started: fastANI
[2023-03-14 14:06:37,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgefb5a42c-0ed2-4ffa-b8df-2eccea7c267e/OceanDNA-b34721.fa --refList OceanDNA-b34721/target_genomes.txt --output OceanDNA-b34721/fastani_result.tsv --threads 1
[2023-03-14 14:06:54,102] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:54,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:06:54,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:06:54,110] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:06:54,110] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:06:54,110] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	79.2649	483	1156	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	78.6798	407	1156	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.6549	414	1156	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.7883	259	1156	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.7052	196	1156	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.3802	137	1156	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.2084	175	1156	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.0479	174	1156	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	76.9928	175	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:06:54,110] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34721/tc_result.tsv
[2023-03-14 14:06:54,110] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:06:54,110] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:06:54,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/checkm_data
[2023-03-14 14:06:54,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:06:54,119] [INFO] Task started: CheckM
[2023-03-14 14:06:54,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34721/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34721/checkm_input OceanDNA-b34721/checkm_result
[2023-03-14 14:07:45,270] [INFO] Task succeeded: CheckM
[2023-03-14 14:07:45,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.87%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:07:45,273] [INFO] ===== Completeness check finished =====
[2023-03-14 14:07:45,273] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:07:45,273] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34721/markers.fasta)
[2023-03-14 14:07:45,274] [INFO] Task started: Blastn
[2023-03-14 14:07:45,274] [INFO] Running command: blastn -query OceanDNA-b34721/markers.fasta -db /var/lib/cwl/stgc8ab3c6c-7aae-4058-a664-a98762548157/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34721/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:07:46,199] [INFO] Task succeeded: Blastn
[2023-03-14 14:07:46,200] [INFO] Selected 8 target genomes.
[2023-03-14 14:07:46,200] [INFO] Target genome list was writen to OceanDNA-b34721/target_genomes_gtdb.txt
[2023-03-14 14:07:46,206] [INFO] Task started: fastANI
[2023-03-14 14:07:46,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgefb5a42c-0ed2-4ffa-b8df-2eccea7c267e/OceanDNA-b34721.fa --refList OceanDNA-b34721/target_genomes_gtdb.txt --output OceanDNA-b34721/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:07:53,219] [INFO] Task succeeded: fastANI
[2023-03-14 14:07:53,225] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:07:53,225] [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
GCF_014077505.1	s__Cognaticolwellia sp014077505	82.9105	766	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	81.7711	718	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	81.7562	690	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	81.6938	660	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	81.6124	710	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	81.5668	659	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	80.8556	647	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	79.2453	485	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:07:53,225] [INFO] GTDB search result was written to OceanDNA-b34721/result_gtdb.tsv
[2023-03-14 14:07:53,225] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:07:53,226] [INFO] DFAST_QC result json was written to OceanDNA-b34721/dqc_result.json
[2023-03-14 14:07:53,226] [INFO] DFAST_QC completed!
[2023-03-14 14:07:53,226] [INFO] Total running time: 0h1m44s