[2023-03-17 02:42:34,227] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:42:34,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:42:34,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference
[2023-03-17 02:42:35,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:42:35,367] [INFO] Task started: Prodigal
[2023-03-17 02:42:35,368] [INFO] Running command: cat /var/lib/cwl/stg4fd813ef-416b-4a6a-ae17-3592982a3c34/OceanDNA-b34753.fa | prodigal -d OceanDNA-b34753/cds.fna -a OceanDNA-b34753/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:42:57,171] [INFO] Task succeeded: Prodigal
[2023-03-17 02:42:57,171] [INFO] Task started: HMMsearch
[2023-03-17 02:42:57,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b34753/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/reference_markers.hmm OceanDNA-b34753/protein.faa > /dev/null
[2023-03-17 02:42:57,401] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:42:57,402] [INFO] Found 6/6 markers.
[2023-03-17 02:42:57,425] [INFO] Query marker FASTA was written to OceanDNA-b34753/markers.fasta
[2023-03-17 02:42:57,426] [INFO] Task started: Blastn
[2023-03-17 02:42:57,427] [INFO] Running command: blastn -query OceanDNA-b34753/markers.fasta -db /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/reference_markers.fasta -out OceanDNA-b34753/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:42:58,076] [INFO] Task succeeded: Blastn
[2023-03-17 02:42:58,077] [INFO] Selected 18 target genomes.
[2023-03-17 02:42:58,077] [INFO] Target genome list was writen to OceanDNA-b34753/target_genomes.txt
[2023-03-17 02:42:58,117] [INFO] Task started: fastANI
[2023-03-17 02:42:58,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd813ef-416b-4a6a-ae17-3592982a3c34/OceanDNA-b34753.fa --refList OceanDNA-b34753/target_genomes.txt --output OceanDNA-b34753/fastani_result.tsv --threads 1
[2023-03-17 02:43:10,676] [INFO] Task succeeded: fastANI
[2023-03-17 02:43:10,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:43:10,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:43:10,685] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:43:10,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:43:10,686] [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	79.625	526	1384	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.2315	419	1384	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.1992	420	1384	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.1318	328	1384	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.0614	267	1384	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9734	218	1384	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.7558	223	1384	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.754	256	1384	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.2867	183	1384	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.4345	58	1384	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.1677	61	1384	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.0628	62	1384	95	below_threshold
Aliivibrio sifiae	strain=NBRC 105001	GCA_002954715.1	566293	566293	type	True	75.7083	58	1384	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:43:10,686] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34753/tc_result.tsv
[2023-03-17 02:43:10,686] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:43:10,686] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:43:10,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/checkm_data
[2023-03-17 02:43:10,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:43:10,714] [INFO] Task started: CheckM
[2023-03-17 02:43:10,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34753/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34753/checkm_input OceanDNA-b34753/checkm_result
[2023-03-17 02:44:04,714] [INFO] Task succeeded: CheckM
[2023-03-17 02:44:04,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:44:04,717] [INFO] ===== Completeness check finished =====
[2023-03-17 02:44:04,717] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:44:04,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34753/markers.fasta)
[2023-03-17 02:44:04,718] [INFO] Task started: Blastn
[2023-03-17 02:44:04,719] [INFO] Running command: blastn -query OceanDNA-b34753/markers.fasta -db /var/lib/cwl/stg9a27d810-f891-454e-a3b4-cff4233f340e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34753/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:44:05,899] [INFO] Task succeeded: Blastn
[2023-03-17 02:44:05,900] [INFO] Selected 9 target genomes.
[2023-03-17 02:44:05,900] [INFO] Target genome list was writen to OceanDNA-b34753/target_genomes_gtdb.txt
[2023-03-17 02:44:05,910] [INFO] Task started: fastANI
[2023-03-17 02:44:05,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd813ef-416b-4a6a-ae17-3592982a3c34/OceanDNA-b34753.fa --refList OceanDNA-b34753/target_genomes_gtdb.txt --output OceanDNA-b34753/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:44:14,433] [INFO] Task succeeded: fastANI
[2023-03-17 02:44:14,440] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:44:14,440] [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_003061515.1	s__Cognaticolwellia sp003061515	98.2435	1263	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	conclusive
GCF_002076895.1	s__Cognaticolwellia beringensis	84.1488	993	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	83.6496	926	1384	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	83.4845	992	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	83.4378	996	1384	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	81.1039	764	1384	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	80.998	758	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	80.9281	743	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	80.2963	651	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:44:14,440] [INFO] GTDB search result was written to OceanDNA-b34753/result_gtdb.tsv
[2023-03-17 02:44:14,440] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:44:14,442] [INFO] DFAST_QC result json was written to OceanDNA-b34753/dqc_result.json
[2023-03-17 02:44:14,442] [INFO] DFAST_QC completed!
[2023-03-17 02:44:14,442] [INFO] Total running time: 0h1m40s