[2023-03-17 06:30:49,106] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,106] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,292] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stgb0cbfad1-6b1f-49ca-803b-aebabdb049fa/OceanDNA-b6756.fa | prodigal -d OceanDNA-b6756/cds.fna -a OceanDNA-b6756/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:06,314] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:06,314] [INFO] Task started: HMMsearch
[2023-03-17 06:31:06,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b6756/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/reference_markers.hmm OceanDNA-b6756/protein.faa > /dev/null
[2023-03-17 06:31:06,514] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:06,515] [INFO] Found 6/6 markers.
[2023-03-17 06:31:06,534] [INFO] Query marker FASTA was written to OceanDNA-b6756/markers.fasta
[2023-03-17 06:31:06,534] [INFO] Task started: Blastn
[2023-03-17 06:31:06,534] [INFO] Running command: blastn -query OceanDNA-b6756/markers.fasta -db /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/reference_markers.fasta -out OceanDNA-b6756/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:07,170] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:07,170] [INFO] Selected 16 target genomes.
[2023-03-17 06:31:07,171] [INFO] Target genome list was writen to OceanDNA-b6756/target_genomes.txt
[2023-03-17 06:31:07,178] [INFO] Task started: fastANI
[2023-03-17 06:31:07,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cbfad1-6b1f-49ca-803b-aebabdb049fa/OceanDNA-b6756.fa --refList OceanDNA-b6756/target_genomes.txt --output OceanDNA-b6756/fastani_result.tsv --threads 1
[2023-03-17 06:31:18,212] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:18,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:18,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:18,222] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:18,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:18,222] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.3443	444	890	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.9861	434	890	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.9605	432	890	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.9599	433	890	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.9484	409	890	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.9451	432	890	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.9356	418	890	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.93	434	890	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.8175	421	890	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.7548	405	890	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.3515	334	890	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.2373	330	890	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.185	377	890	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.0519	282	890	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.8794	294	890	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.7615	285	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:18,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6756/tc_result.tsv
[2023-03-17 06:31:18,223] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:18,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:18,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/checkm_data
[2023-03-17 06:31:18,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:18,228] [INFO] Task started: CheckM
[2023-03-17 06:31:18,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6756/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6756/checkm_input OceanDNA-b6756/checkm_result
[2023-03-17 06:31:59,879] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:59,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:59,881] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:59,882] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:59,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6756/markers.fasta)
[2023-03-17 06:31:59,882] [INFO] Task started: Blastn
[2023-03-17 06:31:59,882] [INFO] Running command: blastn -query OceanDNA-b6756/markers.fasta -db /var/lib/cwl/stgbe454b2c-4ac5-4014-bb23-1f8d2cdea31a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6756/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:00,787] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:00,788] [INFO] Selected 16 target genomes.
[2023-03-17 06:32:00,788] [INFO] Target genome list was writen to OceanDNA-b6756/target_genomes_gtdb.txt
[2023-03-17 06:32:00,932] [INFO] Task started: fastANI
[2023-03-17 06:32:00,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cbfad1-6b1f-49ca-803b-aebabdb049fa/OceanDNA-b6756.fa --refList OceanDNA-b6756/target_genomes_gtdb.txt --output OceanDNA-b6756/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:11,768] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:11,777] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:11,777] [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_900114265.1	s__Flaviramulus basaltis	87.6167	748	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	79.9644	415	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	79.4651	438	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.3622	456	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.3443	444	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	79.3248	390	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	79.0064	417	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.9756	435	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.9482	409	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.9462	416	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.9451	432	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.8175	421	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.7447	406	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.538	378	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	78.0288	284	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.6331	321	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:11,777] [INFO] GTDB search result was written to OceanDNA-b6756/result_gtdb.tsv
[2023-03-17 06:32:11,778] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:11,779] [INFO] DFAST_QC result json was written to OceanDNA-b6756/dqc_result.json
[2023-03-17 06:32:11,779] [INFO] DFAST_QC completed!
[2023-03-17 06:32:11,779] [INFO] Total running time: 0h1m23s