[2023-03-16 18:18:12,464] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference
[2023-03-16 18:18:13,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,554] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,554] [INFO] Running command: cat /var/lib/cwl/stg4c6e1073-a9ac-48b3-bf8d-76162c4b7299/OceanDNA-b11383.fa | prodigal -d OceanDNA-b11383/cds.fna -a OceanDNA-b11383/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:41,487] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:41,487] [INFO] Task started: HMMsearch
[2023-03-16 18:18:41,487] [INFO] Running command: hmmsearch --tblout OceanDNA-b11383/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/reference_markers.hmm OceanDNA-b11383/protein.faa > /dev/null
[2023-03-16 18:18:41,995] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:41,996] [INFO] Found 6/6 markers.
[2023-03-16 18:18:42,030] [INFO] Query marker FASTA was written to OceanDNA-b11383/markers.fasta
[2023-03-16 18:18:42,038] [INFO] Task started: Blastn
[2023-03-16 18:18:42,038] [INFO] Running command: blastn -query OceanDNA-b11383/markers.fasta -db /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/reference_markers.fasta -out OceanDNA-b11383/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:43,854] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:43,855] [INFO] Selected 19 target genomes.
[2023-03-16 18:18:43,855] [INFO] Target genome list was writen to OceanDNA-b11383/target_genomes.txt
[2023-03-16 18:18:43,871] [INFO] Task started: fastANI
[2023-03-16 18:18:43,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c6e1073-a9ac-48b3-bf8d-76162c4b7299/OceanDNA-b11383.fa --refList OceanDNA-b11383/target_genomes.txt --output OceanDNA-b11383/fastani_result.tsv --threads 1
[2023-03-16 18:18:59,764] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:59,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:18:59,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:18:59,776] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:18:59,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:18:59,776] [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
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	84.5276	711	983	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	79.9614	541	983	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	79.4209	461	983	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1835	356	983	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1828	356	983	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.019	298	983	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.9824	311	983	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.7553	268	983	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.7253	280	983	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	77.5013	227	983	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.478	301	983	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.4538	231	983	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.4307	250	983	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	77.3989	222	983	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3091	128	983	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.0129	173	983	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.9622	201	983	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.7377	176	983	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.5404	103	983	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:18:59,777] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11383/tc_result.tsv
[2023-03-16 18:18:59,777] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:18:59,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:18:59,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/checkm_data
[2023-03-16 18:18:59,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:18:59,783] [INFO] Task started: CheckM
[2023-03-16 18:18:59,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11383/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11383/checkm_input OceanDNA-b11383/checkm_result
[2023-03-16 18:19:54,958] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:54,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:54,961] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:54,961] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:54,961] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11383/markers.fasta)
[2023-03-16 18:19:54,962] [INFO] Task started: Blastn
[2023-03-16 18:19:54,963] [INFO] Running command: blastn -query OceanDNA-b11383/markers.fasta -db /var/lib/cwl/stg613ff03c-9fa6-40ba-8cfc-bc215f8cd9a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11383/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:55,908] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:55,909] [INFO] Selected 7 target genomes.
[2023-03-16 18:19:55,909] [INFO] Target genome list was writen to OceanDNA-b11383/target_genomes_gtdb.txt
[2023-03-16 18:19:55,920] [INFO] Task started: fastANI
[2023-03-16 18:19:55,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c6e1073-a9ac-48b3-bf8d-76162c4b7299/OceanDNA-b11383.fa --refList OceanDNA-b11383/target_genomes_gtdb.txt --output OceanDNA-b11383/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:20:00,171] [INFO] Task succeeded: fastANI
[2023-03-16 18:20:00,176] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:20:00,176] [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_004211785.1	s__Winogradskyella sp004211785	99.8475	881	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635865.1	s__Winogradskyella haliclonae	84.5135	712	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	80.731	583	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_905480385.1	s__Winogradskyella sp905480385	80.0189	444	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_013042245.1	s__Winogradskyella sp013042245	79.9766	405	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_900129745.1	s__Winogradskyella jejuensis	79.9559	542	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	79.4339	460	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:20:00,176] [INFO] GTDB search result was written to OceanDNA-b11383/result_gtdb.tsv
[2023-03-16 18:20:00,176] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:20:00,178] [INFO] DFAST_QC result json was written to OceanDNA-b11383/dqc_result.json
[2023-03-16 18:20:00,178] [INFO] DFAST_QC completed!
[2023-03-16 18:20:00,178] [INFO] Total running time: 0h1m48s