[2023-03-17 04:35:35,453] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,454] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,688] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stge481932a-2bf6-4e11-a214-fad899a521b9/OceanDNA-b34664.fa | prodigal -d OceanDNA-b34664/cds.fna -a OceanDNA-b34664/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:55,913] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:55,913] [INFO] Task started: HMMsearch
[2023-03-17 04:35:55,913] [INFO] Running command: hmmsearch --tblout OceanDNA-b34664/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/reference_markers.hmm OceanDNA-b34664/protein.faa > /dev/null
[2023-03-17 04:35:56,104] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:56,104] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge481932a-2bf6-4e11-a214-fad899a521b9/OceanDNA-b34664.fa]
[2023-03-17 04:35:56,126] [INFO] Query marker FASTA was written to OceanDNA-b34664/markers.fasta
[2023-03-17 04:35:56,126] [INFO] Task started: Blastn
[2023-03-17 04:35:56,126] [INFO] Running command: blastn -query OceanDNA-b34664/markers.fasta -db /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/reference_markers.fasta -out OceanDNA-b34664/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:56,655] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:56,656] [INFO] Selected 16 target genomes.
[2023-03-17 04:35:56,656] [INFO] Target genome list was writen to OceanDNA-b34664/target_genomes.txt
[2023-03-17 04:35:56,663] [INFO] Task started: fastANI
[2023-03-17 04:35:56,663] [INFO] Running command: fastANI --query /var/lib/cwl/stge481932a-2bf6-4e11-a214-fad899a521b9/OceanDNA-b34664.fa --refList OceanDNA-b34664/target_genomes.txt --output OceanDNA-b34664/fastani_result.tsv --threads 1
[2023-03-17 04:36:07,821] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:07,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:36:07,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:36:07,828] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:36:07,828] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:36:07,828] [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 demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.4951	378	1240	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.3816	277	1240	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.3113	302	1240	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.3027	262	1240	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.0419	295	1240	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	76.769	102	1240	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	76.7503	75	1240	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	76.2869	63	1240	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	75.4913	56	1240	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:36:07,828] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34664/tc_result.tsv
[2023-03-17 04:36:07,828] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:36:07,829] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:36:07,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/checkm_data
[2023-03-17 04:36:07,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:36:07,834] [INFO] Task started: CheckM
[2023-03-17 04:36:07,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34664/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34664/checkm_input OceanDNA-b34664/checkm_result
[2023-03-17 04:36:56,541] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:56,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:36:56,544] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:56,544] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:56,545] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34664/markers.fasta)
[2023-03-17 04:36:56,545] [INFO] Task started: Blastn
[2023-03-17 04:36:56,545] [INFO] Running command: blastn -query OceanDNA-b34664/markers.fasta -db /var/lib/cwl/stg41f11978-60fa-440e-9a0a-e3168b9961e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34664/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:57,225] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:57,226] [INFO] Selected 9 target genomes.
[2023-03-17 04:36:57,226] [INFO] Target genome list was writen to OceanDNA-b34664/target_genomes_gtdb.txt
[2023-03-17 04:36:57,369] [INFO] Task started: fastANI
[2023-03-17 04:36:57,369] [INFO] Running command: fastANI --query /var/lib/cwl/stge481932a-2bf6-4e11-a214-fad899a521b9/OceanDNA-b34664.fa --refList OceanDNA-b34664/target_genomes_gtdb.txt --output OceanDNA-b34664/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:37:04,778] [INFO] Task succeeded: fastANI
[2023-03-17 04:37:04,784] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:37:04,784] [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_003521815.1	s__Colwellia sp003521815	86.3723	514	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	85.6096	695	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	84.4953	723	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_013215465.1	s__Colwellia sp013215465	83.9031	715	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_007954275.1	s__Colwellia demingiae	79.5086	375	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	78.7843	385	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	78.5835	280	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	78.5501	295	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.1769	296	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:37:04,784] [INFO] GTDB search result was written to OceanDNA-b34664/result_gtdb.tsv
[2023-03-17 04:37:04,784] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:37:04,786] [INFO] DFAST_QC result json was written to OceanDNA-b34664/dqc_result.json
[2023-03-17 04:37:04,786] [INFO] DFAST_QC completed!
[2023-03-17 04:37:04,786] [INFO] Total running time: 0h1m29s