[2023-03-16 00:43:05,200] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:05,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:05,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference
[2023-03-16 00:43:06,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:06,309] [INFO] Task started: Prodigal
[2023-03-16 00:43:06,310] [INFO] Running command: cat /var/lib/cwl/stg2fb6c59c-8a27-402c-a9aa-aeae4919603c/OceanDNA-b7452.fa | prodigal -d OceanDNA-b7452/cds.fna -a OceanDNA-b7452/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:20,739] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:20,739] [INFO] Task started: HMMsearch
[2023-03-16 00:43:20,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b7452/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/reference_markers.hmm OceanDNA-b7452/protein.faa > /dev/null
[2023-03-16 00:43:20,908] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:20,909] [INFO] Found 6/6 markers.
[2023-03-16 00:43:20,925] [INFO] Query marker FASTA was written to OceanDNA-b7452/markers.fasta
[2023-03-16 00:43:20,926] [INFO] Task started: Blastn
[2023-03-16 00:43:20,926] [INFO] Running command: blastn -query OceanDNA-b7452/markers.fasta -db /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/reference_markers.fasta -out OceanDNA-b7452/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:21,531] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:21,533] [INFO] Selected 30 target genomes.
[2023-03-16 00:43:21,533] [INFO] Target genome list was writen to OceanDNA-b7452/target_genomes.txt
[2023-03-16 00:43:21,548] [INFO] Task started: fastANI
[2023-03-16 00:43:21,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb6c59c-8a27-402c-a9aa-aeae4919603c/OceanDNA-b7452.fa --refList OceanDNA-b7452/target_genomes.txt --output OceanDNA-b7452/fastani_result.tsv --threads 1
[2023-03-16 00:43:37,439] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:37,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:37,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:37,446] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:37,446] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:43:37,447] [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
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6372	101	663	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.6336	99	663	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.4258	99	663	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.3413	63	663	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	76.3355	84	663	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.172	75	663	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.1253	93	663	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	75.9388	82	663	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:43:37,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7452/tc_result.tsv
[2023-03-16 00:43:37,449] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:37,449] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:37,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/checkm_data
[2023-03-16 00:43:37,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:37,529] [INFO] Task started: CheckM
[2023-03-16 00:43:37,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7452/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7452/checkm_input OceanDNA-b7452/checkm_result
[2023-03-16 00:44:16,347] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:16,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:16,389] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:16,389] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:16,389] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7452/markers.fasta)
[2023-03-16 00:44:16,391] [INFO] Task started: Blastn
[2023-03-16 00:44:16,391] [INFO] Running command: blastn -query OceanDNA-b7452/markers.fasta -db /var/lib/cwl/stg0bc8918a-9cc0-48cc-b59b-4d451de80b0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7452/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:17,355] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:17,359] [INFO] Selected 33 target genomes.
[2023-03-16 00:44:17,359] [INFO] Target genome list was writen to OceanDNA-b7452/target_genomes_gtdb.txt
[2023-03-16 00:44:17,420] [INFO] Task started: fastANI
[2023-03-16 00:44:17,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb6c59c-8a27-402c-a9aa-aeae4919603c/OceanDNA-b7452.fa --refList OceanDNA-b7452/target_genomes_gtdb.txt --output OceanDNA-b7452/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:34,973] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:34,983] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:34,984] [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
GCF_900102055.1	s__Ulvibacter litoralis	76.6336	99	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.5415	74	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.4387	50	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	76.4258	99	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.3862	84	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476645.1	s__Aequorivita echinoideorum	76.3733	62	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.3726	96	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	76.194	74	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.1861	105	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_016649715.1	s__Aequorivita sp016649715	76.1314	64	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	76.0604	69	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	76.029	77	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	75.9761	69	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_003688405.1	s__Ulvibacter antarcticus	75.9541	81	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	75.9129	53	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	75.8709	76	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	75.668	51	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000170815.1	s__Patiriisocius sp000170815	75.5379	68	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:34,985] [INFO] GTDB search result was written to OceanDNA-b7452/result_gtdb.tsv
[2023-03-16 00:44:34,985] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:34,987] [INFO] DFAST_QC result json was written to OceanDNA-b7452/dqc_result.json
[2023-03-16 00:44:34,988] [INFO] DFAST_QC completed!
[2023-03-16 00:44:34,988] [INFO] Total running time: 0h1m30s