[2023-03-19 01:12:13,941] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,941] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference
[2023-03-19 01:12:15,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:15,733] [INFO] Task started: Prodigal
[2023-03-19 01:12:15,733] [INFO] Running command: cat /var/lib/cwl/stg70b9cb1d-eee9-4962-bd75-37b2fee627e6/OceanDNA-b9977.fa | prodigal -d OceanDNA-b9977/cds.fna -a OceanDNA-b9977/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:27,789] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:27,789] [INFO] Task started: HMMsearch
[2023-03-19 01:12:27,789] [INFO] Running command: hmmsearch --tblout OceanDNA-b9977/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/reference_markers.hmm OceanDNA-b9977/protein.faa > /dev/null
[2023-03-19 01:12:27,928] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:27,928] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg70b9cb1d-eee9-4962-bd75-37b2fee627e6/OceanDNA-b9977.fa]
[2023-03-19 01:12:27,942] [INFO] Query marker FASTA was written to OceanDNA-b9977/markers.fasta
[2023-03-19 01:12:27,942] [INFO] Task started: Blastn
[2023-03-19 01:12:27,942] [INFO] Running command: blastn -query OceanDNA-b9977/markers.fasta -db /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/reference_markers.fasta -out OceanDNA-b9977/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:28,399] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:28,399] [INFO] Selected 7 target genomes.
[2023-03-19 01:12:28,399] [INFO] Target genome list was writen to OceanDNA-b9977/target_genomes.txt
[2023-03-19 01:12:28,403] [INFO] Task started: fastANI
[2023-03-19 01:12:28,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b9cb1d-eee9-4962-bd75-37b2fee627e6/OceanDNA-b9977.fa --refList OceanDNA-b9977/target_genomes.txt --output OceanDNA-b9977/fastani_result.tsv --threads 1
[2023-03-19 01:12:33,200] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:33,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:33,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:33,206] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:33,206] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:12:33,206] [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
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	82.3768	448	704	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	82.1125	454	704	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	82.0748	449	704	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	81.7703	438	704	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	81.2899	421	704	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	81.1866	427	704	95	below_threshold
Polaribacter irgensii	strain=23-P	GCA_000153225.1	531	531	type	True	78.9456	276	704	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:12:33,206] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9977/tc_result.tsv
[2023-03-19 01:12:33,207] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:33,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:33,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/checkm_data
[2023-03-19 01:12:33,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:33,211] [INFO] Task started: CheckM
[2023-03-19 01:12:33,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9977/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9977/checkm_input OceanDNA-b9977/checkm_result
[2023-03-19 01:13:06,331] [INFO] Task succeeded: CheckM
[2023-03-19 01:13:06,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:13:06,333] [INFO] ===== Completeness check finished =====
[2023-03-19 01:13:06,334] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:13:06,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9977/markers.fasta)
[2023-03-19 01:13:06,335] [INFO] Task started: Blastn
[2023-03-19 01:13:06,335] [INFO] Running command: blastn -query OceanDNA-b9977/markers.fasta -db /var/lib/cwl/stg15c6df9b-4f78-4687-9c09-ec98c1319000/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9977/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:06,842] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:06,843] [INFO] Selected 8 target genomes.
[2023-03-19 01:13:06,843] [INFO] Target genome list was writen to OceanDNA-b9977/target_genomes_gtdb.txt
[2023-03-19 01:13:06,848] [INFO] Task started: fastANI
[2023-03-19 01:13:06,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b9cb1d-eee9-4962-bd75-37b2fee627e6/OceanDNA-b9977.fa --refList OceanDNA-b9977/target_genomes_gtdb.txt --output OceanDNA-b9977/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:13:12,039] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:12,045] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:13:12,045] [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_002831685.1	s__Polaribacter sp002831685	84.2364	472	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	83.367	487	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	83.2827	508	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_014352875.1	s__Polaribacter sp014352875	82.3768	448	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	82.0521	451	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905181765.1	s__Polaribacter sp905181765	82.0405	306	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_009796785.1	s__Polaribacter sp009796785	81.6287	445	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	81.3798	409	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:13:12,045] [INFO] GTDB search result was written to OceanDNA-b9977/result_gtdb.tsv
[2023-03-19 01:13:12,045] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:13:12,047] [INFO] DFAST_QC result json was written to OceanDNA-b9977/dqc_result.json
[2023-03-19 01:13:12,047] [INFO] DFAST_QC completed!
[2023-03-19 01:13:12,047] [INFO] Total running time: 0h0m58s