[2023-03-19 05:19:33,647] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,647] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference
[2023-03-19 05:19:34,867] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:34,867] [INFO] Task started: Prodigal
[2023-03-19 05:19:34,867] [INFO] Running command: cat /var/lib/cwl/stg0068ab92-a106-496d-953a-3db25ab86cfc/OceanDNA-b34782.fa | prodigal -d OceanDNA-b34782/cds.fna -a OceanDNA-b34782/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:47,413] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:47,414] [INFO] Task started: HMMsearch
[2023-03-19 05:19:47,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b34782/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/reference_markers.hmm OceanDNA-b34782/protein.faa > /dev/null
[2023-03-19 05:19:47,611] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:47,611] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0068ab92-a106-496d-953a-3db25ab86cfc/OceanDNA-b34782.fa]
[2023-03-19 05:19:47,633] [INFO] Query marker FASTA was written to OceanDNA-b34782/markers.fasta
[2023-03-19 05:19:47,634] [INFO] Task started: Blastn
[2023-03-19 05:19:47,634] [INFO] Running command: blastn -query OceanDNA-b34782/markers.fasta -db /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/reference_markers.fasta -out OceanDNA-b34782/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:48,142] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:48,143] [INFO] Selected 19 target genomes.
[2023-03-19 05:19:48,143] [INFO] Target genome list was writen to OceanDNA-b34782/target_genomes.txt
[2023-03-19 05:19:48,151] [INFO] Task started: fastANI
[2023-03-19 05:19:48,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg0068ab92-a106-496d-953a-3db25ab86cfc/OceanDNA-b34782.fa --refList OceanDNA-b34782/target_genomes.txt --output OceanDNA-b34782/fastani_result.tsv --threads 1
[2023-03-19 05:19:59,995] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:59,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:59,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:00,002] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:00,002] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:00,002] [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	77.4669	104	694	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.9129	101	694	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.8784	118	694	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	76.7907	109	694	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	76.7326	115	694	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	76.7059	94	694	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	76.6475	86	694	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	76.5712	124	694	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	76.4181	93	694	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:00,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34782/tc_result.tsv
[2023-03-19 05:20:00,002] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:00,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:00,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/checkm_data
[2023-03-19 05:20:00,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:00,008] [INFO] Task started: CheckM
[2023-03-19 05:20:00,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34782/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34782/checkm_input OceanDNA-b34782/checkm_result
[2023-03-19 05:20:35,121] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:35,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:35,123] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:35,124] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:35,124] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34782/markers.fasta)
[2023-03-19 05:20:35,124] [INFO] Task started: Blastn
[2023-03-19 05:20:35,124] [INFO] Running command: blastn -query OceanDNA-b34782/markers.fasta -db /var/lib/cwl/stg1971ce10-3494-4f08-8a3b-ae2106345915/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34782/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:35,793] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:35,794] [INFO] Selected 15 target genomes.
[2023-03-19 05:20:35,794] [INFO] Target genome list was writen to OceanDNA-b34782/target_genomes_gtdb.txt
[2023-03-19 05:20:35,863] [INFO] Task started: fastANI
[2023-03-19 05:20:35,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg0068ab92-a106-496d-953a-3db25ab86cfc/OceanDNA-b34782.fa --refList OceanDNA-b34782/target_genomes_gtdb.txt --output OceanDNA-b34782/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:48,198] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:48,207] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:20:48,207] [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_013216005.1	s__JABSOI01 sp013216005	99.183	630	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013216015.1	s__JABSOI01 sp013216015	85.4314	550	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	77.3694	111	694	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	77.1127	115	694	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	77.1036	113	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	77.047	113	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	77.0129	117	694	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	76.9742	102	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765535.1	s__GCA-2401725 sp016765535	76.8374	84	694	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_002104475.1	s__Cognaticolwellia mytili	76.8115	108	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	76.6899	86	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	76.6818	156	694	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_014077505.1	s__Cognaticolwellia sp014077505	76.5983	109	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	76.5648	121	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_004295665.1	s__Litorilituus sediminis	76.4181	93	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:48,207] [INFO] GTDB search result was written to OceanDNA-b34782/result_gtdb.tsv
[2023-03-19 05:20:48,208] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:48,209] [INFO] DFAST_QC result json was written to OceanDNA-b34782/dqc_result.json
[2023-03-19 05:20:48,209] [INFO] DFAST_QC completed!
[2023-03-19 05:20:48,209] [INFO] Total running time: 0h1m15s