[2024-01-24 13:40:34,916] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,917] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,918] [INFO] DQC Reference Directory: /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference
[2024-01-24 13:40:36,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,287] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg693ec198-367e-489a-baef-f61ad43b96ac/GCF_020463795.1_ASM2046379v1_genomic.fna.gz | prodigal -d GCF_020463795.1_ASM2046379v1_genomic.fna/cds.fna -a GCF_020463795.1_ASM2046379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:03,447] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:03,448] [INFO] Task started: HMMsearch
[2024-01-24 13:41:03,448] [INFO] Running command: hmmsearch --tblout GCF_020463795.1_ASM2046379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/reference_markers.hmm GCF_020463795.1_ASM2046379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:03,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:03,829] [INFO] Found 6/6 markers.
[2024-01-24 13:41:03,876] [INFO] Query marker FASTA was written to GCF_020463795.1_ASM2046379v1_genomic.fna/markers.fasta
[2024-01-24 13:41:03,876] [INFO] Task started: Blastn
[2024-01-24 13:41:03,876] [INFO] Running command: blastn -query GCF_020463795.1_ASM2046379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/reference_markers.fasta -out GCF_020463795.1_ASM2046379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:04,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:04,530] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:04,530] [INFO] Target genome list was writen to GCF_020463795.1_ASM2046379v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:04,536] [INFO] Task started: fastANI
[2024-01-24 13:41:04,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg693ec198-367e-489a-baef-f61ad43b96ac/GCF_020463795.1_ASM2046379v1_genomic.fna.gz --refList GCF_020463795.1_ASM2046379v1_genomic.fna/target_genomes.txt --output GCF_020463795.1_ASM2046379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:19,247] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:19,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:19,257] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:19,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:19,257] [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
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	100.0	1894	1897	95	conclusive
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	86.1204	1277	1897	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	85.1203	1249	1897	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	81.0985	486	1897	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	79.7484	642	1897	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	78.6325	415	1897	95	below_threshold
Echinicola soli	strain=LN3S3	GCA_006575665.1	2591634	2591634	type	True	78.4457	410	1897	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	77.4944	300	1897	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.2473	99	1897	95	below_threshold
Algoriphagus marinus	strain=am2	GCA_001936475.1	1925762	1925762	type	True	75.7091	92	1897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,259] [INFO] DFAST Taxonomy check result was written to GCF_020463795.1_ASM2046379v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:19,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:19,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:19,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/checkm_data
[2024-01-24 13:41:19,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:19,319] [INFO] Task started: CheckM
[2024-01-24 13:41:19,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020463795.1_ASM2046379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020463795.1_ASM2046379v1_genomic.fna/checkm_input GCF_020463795.1_ASM2046379v1_genomic.fna/checkm_result
[2024-01-24 13:42:35,731] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:35,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:35,757] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:35,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:35,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020463795.1_ASM2046379v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:35,758] [INFO] Task started: Blastn
[2024-01-24 13:42:35,758] [INFO] Running command: blastn -query GCF_020463795.1_ASM2046379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga89cebfe-722e-4417-8852-e7087956dea8/dqc_reference/reference_markers_gtdb.fasta -out GCF_020463795.1_ASM2046379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:36,566] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:36,570] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:36,570] [INFO] Target genome list was writen to GCF_020463795.1_ASM2046379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:36,622] [INFO] Task started: fastANI
[2024-01-24 13:42:36,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg693ec198-367e-489a-baef-f61ad43b96ac/GCF_020463795.1_ASM2046379v1_genomic.fna.gz --refList GCF_020463795.1_ASM2046379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020463795.1_ASM2046379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:50,356] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:50,377] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:50,378] [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_014280965.1	s__Echinicola sp014280965	86.1416	1275	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	85.1271	1247	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325705.1	s__Echinicola vietnamensis	81.1055	485	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015533855.1	s__Echinicola sp015533855	79.8004	636	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	79.722	647	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260975.1	s__Echinicola strongylocentroti	78.6339	416	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	78.4196	409	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373245.1	s__Echinicola pacifica	77.5002	295	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.7389	111	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014324365.1	s__Algoriphagus sp014324365	76.5906	69	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.2473	99	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936475.1	s__Algoriphagus marinus	75.7091	92	1897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:50,380] [INFO] GTDB search result was written to GCF_020463795.1_ASM2046379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:50,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:50,386] [INFO] DFAST_QC result json was written to GCF_020463795.1_ASM2046379v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:50,386] [INFO] DFAST_QC completed!
[2024-01-24 13:42:50,386] [INFO] Total running time: 0h2m15s