[2023-03-15 10:09:49,678] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stg4f17cfb9-9718-462a-a490-ac51662c75c5/OceanDNA-b34670.fa | prodigal -d OceanDNA-b34670/cds.fna -a OceanDNA-b34670/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:01,866] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:01,866] [INFO] Task started: HMMsearch
[2023-03-15 10:10:01,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b34670/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/reference_markers.hmm OceanDNA-b34670/protein.faa > /dev/null
[2023-03-15 10:10:02,023] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:02,023] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4f17cfb9-9718-462a-a490-ac51662c75c5/OceanDNA-b34670.fa]
[2023-03-15 10:10:02,036] [INFO] Query marker FASTA was written to OceanDNA-b34670/markers.fasta
[2023-03-15 10:10:02,036] [INFO] Task started: Blastn
[2023-03-15 10:10:02,036] [INFO] Running command: blastn -query OceanDNA-b34670/markers.fasta -db /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/reference_markers.fasta -out OceanDNA-b34670/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:02,534] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:02,535] [INFO] Selected 19 target genomes.
[2023-03-15 10:10:02,535] [INFO] Target genome list was writen to OceanDNA-b34670/target_genomes.txt
[2023-03-15 10:10:02,578] [INFO] Task started: fastANI
[2023-03-15 10:10:02,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f17cfb9-9718-462a-a490-ac51662c75c5/OceanDNA-b34670.fa --refList OceanDNA-b34670/target_genomes.txt --output OceanDNA-b34670/fastani_result.tsv --threads 1
[2023-03-15 10:10:15,790] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:15,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:15,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:15,799] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:15,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:10:15,800] [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 ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.1287	178	662	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.9374	197	662	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.8688	164	662	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.853	154	662	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.8239	153	662	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.48	169	662	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.4055	166	662	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.3775	119	662	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.3642	125	662	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.2151	92	662	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.171	96	662	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.1565	117	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:10:15,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34670/tc_result.tsv
[2023-03-15 10:10:15,800] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:15,800] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:15,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/checkm_data
[2023-03-15 10:10:15,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:15,804] [INFO] Task started: CheckM
[2023-03-15 10:10:15,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34670/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34670/checkm_input OceanDNA-b34670/checkm_result
[2023-03-15 10:10:45,341] [INFO] Task succeeded: CheckM
[2023-03-15 10:10:45,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:10:45,428] [INFO] ===== Completeness check finished =====
[2023-03-15 10:10:45,428] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:10:45,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34670/markers.fasta)
[2023-03-15 10:10:45,430] [INFO] Task started: Blastn
[2023-03-15 10:10:45,430] [INFO] Running command: blastn -query OceanDNA-b34670/markers.fasta -db /var/lib/cwl/stg4795dd79-c5df-4018-b33c-48506ea5f2c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34670/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:46,105] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:46,109] [INFO] Selected 15 target genomes.
[2023-03-15 10:10:46,109] [INFO] Target genome list was writen to OceanDNA-b34670/target_genomes_gtdb.txt
[2023-03-15 10:10:46,561] [INFO] Task started: fastANI
[2023-03-15 10:10:46,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f17cfb9-9718-462a-a490-ac51662c75c5/OceanDNA-b34670.fa --refList OceanDNA-b34670/target_genomes_gtdb.txt --output OceanDNA-b34670/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:10:56,184] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:56,194] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:10:56,194] [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_016745015.1	s__Colwellia sp016745015	80.1042	286	662	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	79.6391	330	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	79.4923	316	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	79.0228	251	662	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	78.8147	258	662	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	78.7813	199	662	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	78.722	268	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	78.5834	201	662	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	78.5659	273	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_018860755.1	s__Colwellia sp018860755	78.1476	164	662	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	78.1287	178	662	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	77.9429	164	662	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	77.8018	154	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	77.7802	193	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.6462	121	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:10:56,196] [INFO] GTDB search result was written to OceanDNA-b34670/result_gtdb.tsv
[2023-03-15 10:10:56,199] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:10:56,202] [INFO] DFAST_QC result json was written to OceanDNA-b34670/dqc_result.json
[2023-03-15 10:10:56,202] [INFO] DFAST_QC completed!
[2023-03-15 10:10:56,202] [INFO] Total running time: 0h1m7s