[2023-03-15 10:49:28,638] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference
[2023-03-15 10:49:29,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,802] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,802] [INFO] Running command: cat /var/lib/cwl/stg852bbace-b486-4640-835f-e9798e23a238/OceanDNA-b11387.fa | prodigal -d OceanDNA-b11387/cds.fna -a OceanDNA-b11387/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:45,947] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:45,947] [INFO] Task started: HMMsearch
[2023-03-15 10:49:45,947] [INFO] Running command: hmmsearch --tblout OceanDNA-b11387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/reference_markers.hmm OceanDNA-b11387/protein.faa > /dev/null
[2023-03-15 10:49:46,193] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:46,194] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg852bbace-b486-4640-835f-e9798e23a238/OceanDNA-b11387.fa]
[2023-03-15 10:49:46,214] [INFO] Query marker FASTA was written to OceanDNA-b11387/markers.fasta
[2023-03-15 10:49:46,215] [INFO] Task started: Blastn
[2023-03-15 10:49:46,215] [INFO] Running command: blastn -query OceanDNA-b11387/markers.fasta -db /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/reference_markers.fasta -out OceanDNA-b11387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:46,857] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:46,858] [INFO] Selected 19 target genomes.
[2023-03-15 10:49:46,858] [INFO] Target genome list was writen to OceanDNA-b11387/target_genomes.txt
[2023-03-15 10:49:46,869] [INFO] Task started: fastANI
[2023-03-15 10:49:46,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg852bbace-b486-4640-835f-e9798e23a238/OceanDNA-b11387.fa --refList OceanDNA-b11387/target_genomes.txt --output OceanDNA-b11387/fastani_result.tsv --threads 1
[2023-03-15 10:49:59,582] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:59,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:59,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:59,593] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:59,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:49:59,593] [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 ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.8866	289	840	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.6238	267	840	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.5186	302	840	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.5086	284	840	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	78.4556	288	840	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.346	275	840	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	78.2164	255	840	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.1745	275	840	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.173	263	840	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.0663	252	840	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.9123	254	840	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.8579	252	840	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	77.7842	198	840	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.7543	198	840	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6159	95	840	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.4429	83	840	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4362	80	840	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3381	92	840	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:49:59,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11387/tc_result.tsv
[2023-03-15 10:49:59,594] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:59,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:59,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/checkm_data
[2023-03-15 10:49:59,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:59,600] [INFO] Task started: CheckM
[2023-03-15 10:49:59,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11387/checkm_input OceanDNA-b11387/checkm_result
[2023-03-15 10:50:42,100] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:42,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:42,103] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:42,103] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:42,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11387/markers.fasta)
[2023-03-15 10:50:42,104] [INFO] Task started: Blastn
[2023-03-15 10:50:42,105] [INFO] Running command: blastn -query OceanDNA-b11387/markers.fasta -db /var/lib/cwl/stg416ce44d-d057-4d5d-8eda-192d8fccf7b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:42,929] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:42,930] [INFO] Selected 12 target genomes.
[2023-03-15 10:50:42,930] [INFO] Target genome list was writen to OceanDNA-b11387/target_genomes_gtdb.txt
[2023-03-15 10:50:42,944] [INFO] Task started: fastANI
[2023-03-15 10:50:42,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg852bbace-b486-4640-835f-e9798e23a238/OceanDNA-b11387.fa --refList OceanDNA-b11387/target_genomes_gtdb.txt --output OceanDNA-b11387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:50,865] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:50,872] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:50:50,872] [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_016744625.1	s__Winogradskyella sp016744625	80.5137	375	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	80.1754	355	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	79.0928	343	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	78.8936	288	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.7922	317	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	78.7041	297	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.6388	301	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	78.5321	301	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	78.4778	288	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.3459	275	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	78.301	262	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	77.9123	254	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:50,873] [INFO] GTDB search result was written to OceanDNA-b11387/result_gtdb.tsv
[2023-03-15 10:50:50,873] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:50,875] [INFO] DFAST_QC result json was written to OceanDNA-b11387/dqc_result.json
[2023-03-15 10:50:50,875] [INFO] DFAST_QC completed!
[2023-03-15 10:50:50,875] [INFO] Total running time: 0h1m22s