[2023-03-17 11:57:21,087] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:21,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:21,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference
[2023-03-17 11:57:22,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:22,191] [INFO] Task started: Prodigal
[2023-03-17 11:57:22,191] [INFO] Running command: cat /var/lib/cwl/stg04c80370-e565-4c73-a11c-9b305a73deab/OceanDNA-b34726.fa | prodigal -d OceanDNA-b34726/cds.fna -a OceanDNA-b34726/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:48,107] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:48,107] [INFO] Task started: HMMsearch
[2023-03-17 11:57:48,107] [INFO] Running command: hmmsearch --tblout OceanDNA-b34726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/reference_markers.hmm OceanDNA-b34726/protein.faa > /dev/null
[2023-03-17 11:57:48,358] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:48,359] [INFO] Found 6/6 markers.
[2023-03-17 11:57:48,386] [INFO] Query marker FASTA was written to OceanDNA-b34726/markers.fasta
[2023-03-17 11:57:48,387] [INFO] Task started: Blastn
[2023-03-17 11:57:48,387] [INFO] Running command: blastn -query OceanDNA-b34726/markers.fasta -db /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/reference_markers.fasta -out OceanDNA-b34726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:49,037] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:49,038] [INFO] Selected 27 target genomes.
[2023-03-17 11:57:49,038] [INFO] Target genome list was writen to OceanDNA-b34726/target_genomes.txt
[2023-03-17 11:57:49,051] [INFO] Task started: fastANI
[2023-03-17 11:57:49,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c80370-e565-4c73-a11c-9b305a73deab/OceanDNA-b34726.fa --refList OceanDNA-b34726/target_genomes.txt --output OceanDNA-b34726/fastani_result.tsv --threads 1
[2023-03-17 11:58:08,303] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:08,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:58:08,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:58:08,313] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:58:08,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:58:08,313] [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
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	81.6222	680	1650	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.2714	261	1650	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.9955	256	1650	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.7841	224	1650	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.628	188	1650	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.3649	195	1650	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.3027	269	1650	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.076	160	1650	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.058	206	1650	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.9332	173	1650	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.8866	170	1650	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.8266	192	1650	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	77.7481	105	1650	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	77.6936	80	1650	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	77.6755	108	1650	95	below_threshold
Moritella marina	strain=MP-1	GCA_000381865.1	90736	90736	type	True	75.9499	51	1650	95	below_threshold
Moritella marina	strain=MP-1	GCA_008931805.1	90736	90736	type	True	75.8509	55	1650	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:58:08,313] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34726/tc_result.tsv
[2023-03-17 11:58:08,314] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:58:08,314] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:58:08,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/checkm_data
[2023-03-17 11:58:08,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:58:08,322] [INFO] Task started: CheckM
[2023-03-17 11:58:08,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34726/checkm_input OceanDNA-b34726/checkm_result
[2023-03-17 11:59:11,436] [INFO] Task succeeded: CheckM
[2023-03-17 11:59:11,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:59:11,440] [INFO] ===== Completeness check finished =====
[2023-03-17 11:59:11,440] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:59:11,440] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34726/markers.fasta)
[2023-03-17 11:59:11,440] [INFO] Task started: Blastn
[2023-03-17 11:59:11,440] [INFO] Running command: blastn -query OceanDNA-b34726/markers.fasta -db /var/lib/cwl/stgd2875ced-c763-4059-9231-e8c0555841a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:59:12,458] [INFO] Task succeeded: Blastn
[2023-03-17 11:59:12,459] [INFO] Selected 13 target genomes.
[2023-03-17 11:59:12,459] [INFO] Target genome list was writen to OceanDNA-b34726/target_genomes_gtdb.txt
[2023-03-17 11:59:12,469] [INFO] Task started: fastANI
[2023-03-17 11:59:12,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c80370-e565-4c73-a11c-9b305a73deab/OceanDNA-b34726.fa --refList OceanDNA-b34726/target_genomes_gtdb.txt --output OceanDNA-b34726/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:59:23,409] [INFO] Task succeeded: fastANI
[2023-03-17 11:59:23,416] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:59:23,416] [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_013215295.1	s__Colwellia_A sp013215295	99.9787	1612	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215385.1	s__Colwellia_A sp013215385	82.7448	734	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	81.8569	708	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_007954355.1	s__Colwellia_A hornerae	81.6244	680	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_001767295.1	s__Colwellia_A sp001767295	81.3444	694	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_000378625.1	s__Colwellia piezophila	79.0106	256	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	78.842	273	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545415.1	s__Colwellia sp003545415	78.7675	218	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	78.6057	189	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	78.4074	230	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001831495.1	s__Thalassotalea_A crassostreae	77.6755	108	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018219155.1	s__Moritella sp018219155	76.2607	68	1650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:59:23,417] [INFO] GTDB search result was written to OceanDNA-b34726/result_gtdb.tsv
[2023-03-17 11:59:23,417] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:59:23,418] [INFO] DFAST_QC result json was written to OceanDNA-b34726/dqc_result.json
[2023-03-17 11:59:23,418] [INFO] DFAST_QC completed!
[2023-03-17 11:59:23,418] [INFO] Total running time: 0h2m2s