[2023-03-19 01:33:27,204] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,204] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference
[2023-03-19 01:33:28,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,288] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,288] [INFO] Running command: cat /var/lib/cwl/stg2cac4271-ec0f-404d-9a5b-297ae8966d9f/OceanDNA-b6702.fa | prodigal -d OceanDNA-b6702/cds.fna -a OceanDNA-b6702/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:40,718] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:40,718] [INFO] Task started: HMMsearch
[2023-03-19 01:33:40,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b6702/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/reference_markers.hmm OceanDNA-b6702/protein.faa > /dev/null
[2023-03-19 01:33:40,885] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:40,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2cac4271-ec0f-404d-9a5b-297ae8966d9f/OceanDNA-b6702.fa]
[2023-03-19 01:33:40,900] [INFO] Query marker FASTA was written to OceanDNA-b6702/markers.fasta
[2023-03-19 01:33:40,901] [INFO] Task started: Blastn
[2023-03-19 01:33:40,902] [INFO] Running command: blastn -query OceanDNA-b6702/markers.fasta -db /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/reference_markers.fasta -out OceanDNA-b6702/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:41,484] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:41,485] [INFO] Selected 26 target genomes.
[2023-03-19 01:33:41,485] [INFO] Target genome list was writen to OceanDNA-b6702/target_genomes.txt
[2023-03-19 01:33:41,500] [INFO] Task started: fastANI
[2023-03-19 01:33:41,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cac4271-ec0f-404d-9a5b-297ae8966d9f/OceanDNA-b6702.fa --refList OceanDNA-b6702/target_genomes.txt --output OceanDNA-b6702/fastani_result.tsv --threads 1
[2023-03-19 01:33:56,704] [INFO] Task succeeded: fastANI
[2023-03-19 01:33:56,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:33:56,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:33:56,711] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:33:56,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:33:56,712] [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
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	76.2166	75	595	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	76.0619	97	595	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.0505	95	595	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	75.8414	64	595	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	75.7771	68	595	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	75.6765	50	595	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	75.5846	53	595	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	75.5658	54	595	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	75.3213	52	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:33:56,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6702/tc_result.tsv
[2023-03-19 01:33:56,712] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:33:56,712] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:33:56,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/checkm_data
[2023-03-19 01:33:56,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:33:56,717] [INFO] Task started: CheckM
[2023-03-19 01:33:56,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6702/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6702/checkm_input OceanDNA-b6702/checkm_result
[2023-03-19 01:34:32,233] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:32,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:32,236] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:32,236] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:32,236] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6702/markers.fasta)
[2023-03-19 01:34:32,237] [INFO] Task started: Blastn
[2023-03-19 01:34:32,237] [INFO] Running command: blastn -query OceanDNA-b6702/markers.fasta -db /var/lib/cwl/stg44ac3f98-7a7d-4c0f-b916-81c328a33cf0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6702/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:33,291] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:33,292] [INFO] Selected 28 target genomes.
[2023-03-19 01:34:33,292] [INFO] Target genome list was writen to OceanDNA-b6702/target_genomes_gtdb.txt
[2023-03-19 01:34:33,345] [INFO] Task started: fastANI
[2023-03-19 01:34:33,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cac4271-ec0f-404d-9a5b-297ae8966d9f/OceanDNA-b6702.fa --refList OceanDNA-b6702/target_genomes_gtdb.txt --output OceanDNA-b6702/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:34:49,281] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:49,287] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:34:49,288] [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_009797885.1	s__Croceivirga sp009797885	76.4841	74	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072105.2	s__Croceivirga radicis	76.2166	75	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.98	97.98	0.93	0.93	2	-
GCF_005144745.1	s__Croceivirga sp005144745	76.1053	64	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_014235875.1	s__Croceivirga lutea	76.0619	97	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013001145.1	s__Croceitalea sp013001145	75.8714	59	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_009797025.1	s__Cellulophaga sp009797025	75.7002	53	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	75.6765	50	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	75.6208	57	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	75.5658	54	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000190595.1	s__Cellulophaga lytica	75.5232	52	595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
--------------------------------------------------------------------------------
[2023-03-19 01:34:49,288] [INFO] GTDB search result was written to OceanDNA-b6702/result_gtdb.tsv
[2023-03-19 01:34:49,288] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:34:49,289] [INFO] DFAST_QC result json was written to OceanDNA-b6702/dqc_result.json
[2023-03-19 01:34:49,289] [INFO] DFAST_QC completed!
[2023-03-19 01:34:49,289] [INFO] Total running time: 0h1m22s