[2023-03-16 10:07:19,370] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:07:19,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:07:19,370] [INFO] DQC Reference Directory: /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference
[2023-03-16 10:07:20,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:07:20,446] [INFO] Task started: Prodigal
[2023-03-16 10:07:20,446] [INFO] Running command: cat /var/lib/cwl/stgc55db50e-2231-4575-bf13-6fd1fadc9054/OceanDNA-b34662.fa | prodigal -d OceanDNA-b34662/cds.fna -a OceanDNA-b34662/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:07:44,684] [INFO] Task succeeded: Prodigal
[2023-03-16 10:07:44,684] [INFO] Task started: HMMsearch
[2023-03-16 10:07:44,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b34662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/reference_markers.hmm OceanDNA-b34662/protein.faa > /dev/null
[2023-03-16 10:07:44,923] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:07:44,924] [INFO] Found 6/6 markers.
[2023-03-16 10:07:44,952] [INFO] Query marker FASTA was written to OceanDNA-b34662/markers.fasta
[2023-03-16 10:07:44,953] [INFO] Task started: Blastn
[2023-03-16 10:07:44,953] [INFO] Running command: blastn -query OceanDNA-b34662/markers.fasta -db /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/reference_markers.fasta -out OceanDNA-b34662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:07:45,622] [INFO] Task succeeded: Blastn
[2023-03-16 10:07:45,623] [INFO] Selected 12 target genomes.
[2023-03-16 10:07:45,623] [INFO] Target genome list was writen to OceanDNA-b34662/target_genomes.txt
[2023-03-16 10:07:45,629] [INFO] Task started: fastANI
[2023-03-16 10:07:45,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55db50e-2231-4575-bf13-6fd1fadc9054/OceanDNA-b34662.fa --refList OceanDNA-b34662/target_genomes.txt --output OceanDNA-b34662/fastani_result.tsv --threads 1
[2023-03-16 10:07:55,851] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:55,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:07:55,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:07:55,858] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:07:55,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:07:55,858] [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 piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	84.2098	934	1557	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	83.5837	904	1557	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	81.4631	804	1557	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	79.2403	519	1557	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.5581	451	1557	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.4856	314	1557	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.6629	162	1557	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	76.4598	118	1557	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:07:55,859] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34662/tc_result.tsv
[2023-03-16 10:07:55,859] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:07:55,859] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:07:55,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/checkm_data
[2023-03-16 10:07:55,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:07:55,866] [INFO] Task started: CheckM
[2023-03-16 10:07:55,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34662/checkm_input OceanDNA-b34662/checkm_result
[2023-03-16 10:08:55,147] [INFO] Task succeeded: CheckM
[2023-03-16 10:08:55,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:08:55,151] [INFO] ===== Completeness check finished =====
[2023-03-16 10:08:55,151] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:08:55,151] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34662/markers.fasta)
[2023-03-16 10:08:55,152] [INFO] Task started: Blastn
[2023-03-16 10:08:55,152] [INFO] Running command: blastn -query OceanDNA-b34662/markers.fasta -db /var/lib/cwl/stgbec6fa75-8cfd-49dd-b459-5915ba097017/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:56,178] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:56,179] [INFO] Selected 15 target genomes.
[2023-03-16 10:08:56,179] [INFO] Target genome list was writen to OceanDNA-b34662/target_genomes_gtdb.txt
[2023-03-16 10:08:56,224] [INFO] Task started: fastANI
[2023-03-16 10:08:56,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55db50e-2231-4575-bf13-6fd1fadc9054/OceanDNA-b34662.fa --refList OceanDNA-b34662/target_genomes_gtdb.txt --output OceanDNA-b34662/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:12,349] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:12,358] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:09:12,358] [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_013214175.1	s__Colwellia sp013214175	84.4254	1046	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_000378625.1	s__Colwellia piezophila	84.2212	932	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440345.1	s__Colwellia sp001440345	83.7282	886	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002207865.1	s__Colwellia marinimaniae	83.5662	907	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	82.4693	994	1557	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	81.6289	921	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	81.4801	873	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	81.4791	741	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	81.4597	805	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	81.267	794	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_003545415.1	s__Colwellia sp003545415	80.8722	570	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	79.8149	717	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	78.6686	353	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCA_002733765.1	s__Colwellia sp002733765	78.1285	299	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.6244	281	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:09:12,359] [INFO] GTDB search result was written to OceanDNA-b34662/result_gtdb.tsv
[2023-03-16 10:09:12,359] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:12,360] [INFO] DFAST_QC result json was written to OceanDNA-b34662/dqc_result.json
[2023-03-16 10:09:12,360] [INFO] DFAST_QC completed!
[2023-03-16 10:09:12,360] [INFO] Total running time: 0h1m53s