[2023-03-16 14:26:33,890] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:26:33,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:26:33,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference
[2023-03-16 14:26:36,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:26:36,565] [INFO] Task started: Prodigal
[2023-03-16 14:26:36,565] [INFO] Running command: cat /var/lib/cwl/stgce302c8e-9025-4001-a444-3a50f532bf54/OceanDNA-b34632.fa | prodigal -d OceanDNA-b34632/cds.fna -a OceanDNA-b34632/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:26:50,750] [INFO] Task succeeded: Prodigal
[2023-03-16 14:26:50,751] [INFO] Task started: HMMsearch
[2023-03-16 14:26:50,751] [INFO] Running command: hmmsearch --tblout OceanDNA-b34632/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/reference_markers.hmm OceanDNA-b34632/protein.faa > /dev/null
[2023-03-16 14:26:50,949] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:26:50,949] [INFO] Found 6/6 markers.
[2023-03-16 14:26:50,966] [INFO] Query marker FASTA was written to OceanDNA-b34632/markers.fasta
[2023-03-16 14:26:50,966] [INFO] Task started: Blastn
[2023-03-16 14:26:50,966] [INFO] Running command: blastn -query OceanDNA-b34632/markers.fasta -db /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/reference_markers.fasta -out OceanDNA-b34632/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:26:51,581] [INFO] Task succeeded: Blastn
[2023-03-16 14:26:51,582] [INFO] Selected 17 target genomes.
[2023-03-16 14:26:51,582] [INFO] Target genome list was writen to OceanDNA-b34632/target_genomes.txt
[2023-03-16 14:26:51,590] [INFO] Task started: fastANI
[2023-03-16 14:26:51,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgce302c8e-9025-4001-a444-3a50f532bf54/OceanDNA-b34632.fa --refList OceanDNA-b34632/target_genomes.txt --output OceanDNA-b34632/fastani_result.tsv --threads 1
[2023-03-16 14:27:03,526] [INFO] Task succeeded: fastANI
[2023-03-16 14:27:03,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:27:03,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:27:03,534] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:27:03,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 14:27:03,535] [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	77.8767	206	899	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.7203	171	899	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.6449	197	899	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.602	180	899	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.5602	203	899	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.4886	190	899	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4393	171	899	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	76.8675	120	899	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	76.5361	79	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 14:27:03,535] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34632/tc_result.tsv
[2023-03-16 14:27:03,535] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:27:03,535] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:27:03,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/checkm_data
[2023-03-16 14:27:03,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:27:03,540] [INFO] Task started: CheckM
[2023-03-16 14:27:03,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34632/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34632/checkm_input OceanDNA-b34632/checkm_result
[2023-03-16 14:27:54,383] [INFO] Task succeeded: CheckM
[2023-03-16 14:27:54,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:27:54,386] [INFO] ===== Completeness check finished =====
[2023-03-16 14:27:54,386] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:27:54,386] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34632/markers.fasta)
[2023-03-16 14:27:54,388] [INFO] Task started: Blastn
[2023-03-16 14:27:54,388] [INFO] Running command: blastn -query OceanDNA-b34632/markers.fasta -db /var/lib/cwl/stg01806ea4-7575-453b-843a-291961d50ea9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34632/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:27:55,410] [INFO] Task succeeded: Blastn
[2023-03-16 14:27:55,411] [INFO] Selected 29 target genomes.
[2023-03-16 14:27:55,411] [INFO] Target genome list was writen to OceanDNA-b34632/target_genomes_gtdb.txt
[2023-03-16 14:27:56,050] [INFO] Task started: fastANI
[2023-03-16 14:27:56,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgce302c8e-9025-4001-a444-3a50f532bf54/OceanDNA-b34632.fa --refList OceanDNA-b34632/target_genomes_gtdb.txt --output OceanDNA-b34632/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:28:21,979] [INFO] Task succeeded: fastANI
[2023-03-16 14:28:21,993] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:28:21,994] [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	78.4113	158	899	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	78.0717	181	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	78.0168	201	899	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	77.9442	219	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_007954275.1	s__Colwellia demingiae	77.8764	206	899	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	77.8019	175	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	77.7536	180	899	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	77.7378	203	899	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	77.7209	198	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.7203	171	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.7199	177	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	77.6449	197	899	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_009832865.1	s__Colwellia sp009832865	77.6312	204	899	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	77.6263	185	899	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	77.5849	181	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCF_005885605.1	s__Colwellia ponticola	77.5646	202	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.5553	224	899	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_000764185.1	s__Colwellia psychrerythraea_B	77.5031	201	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378625.1	s__Colwellia piezophila	77.4894	190	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.4891	163	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013216015.1	s__JABSOI01 sp013216015	77.4634	201	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	77.4602	186	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216005.1	s__JABSOI01 sp013216005	77.2856	170	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.2657	149	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	76.7531	115	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	76.5361	79	899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 14:28:21,994] [INFO] GTDB search result was written to OceanDNA-b34632/result_gtdb.tsv
[2023-03-16 14:28:21,994] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:28:21,996] [INFO] DFAST_QC result json was written to OceanDNA-b34632/dqc_result.json
[2023-03-16 14:28:21,996] [INFO] DFAST_QC completed!
[2023-03-16 14:28:21,996] [INFO] Total running time: 0h1m48s