[2024-01-24 13:28:19,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference
[2024-01-24 13:28:20,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,818] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg6146d106-7e33-4bea-ae80-2142728863ec/GCF_014280965.1_ASM1428096v1_genomic.fna.gz | prodigal -d GCF_014280965.1_ASM1428096v1_genomic.fna/cds.fna -a GCF_014280965.1_ASM1428096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:44,249] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:44,249] [INFO] Task started: HMMsearch
[2024-01-24 13:28:44,249] [INFO] Running command: hmmsearch --tblout GCF_014280965.1_ASM1428096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/reference_markers.hmm GCF_014280965.1_ASM1428096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:44,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:44,595] [INFO] Found 6/6 markers.
[2024-01-24 13:28:44,642] [INFO] Query marker FASTA was written to GCF_014280965.1_ASM1428096v1_genomic.fna/markers.fasta
[2024-01-24 13:28:44,643] [INFO] Task started: Blastn
[2024-01-24 13:28:44,643] [INFO] Running command: blastn -query GCF_014280965.1_ASM1428096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/reference_markers.fasta -out GCF_014280965.1_ASM1428096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:45,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:45,272] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:45,273] [INFO] Target genome list was writen to GCF_014280965.1_ASM1428096v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:45,282] [INFO] Task started: fastANI
[2024-01-24 13:28:45,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg6146d106-7e33-4bea-ae80-2142728863ec/GCF_014280965.1_ASM1428096v1_genomic.fna.gz --refList GCF_014280965.1_ASM1428096v1_genomic.fna/target_genomes.txt --output GCF_014280965.1_ASM1428096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:57,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:57,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:57,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:57,477] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:57,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:57,477] [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 salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	100.0	1699	1701	95	conclusive
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	86.1579	1269	1701	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	85.3952	1362	1701	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	79.6439	624	1701	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	77.6179	401	1701	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	77.5623	299	1701	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.5894	128	1701	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.4165	99	1701	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.182	66	1701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,479] [INFO] DFAST Taxonomy check result was written to GCF_014280965.1_ASM1428096v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:57,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:57,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:57,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/checkm_data
[2024-01-24 13:28:57,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:57,536] [INFO] Task started: CheckM
[2024-01-24 13:28:57,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014280965.1_ASM1428096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014280965.1_ASM1428096v1_genomic.fna/checkm_input GCF_014280965.1_ASM1428096v1_genomic.fna/checkm_result
[2024-01-24 13:30:02,630] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:02,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:02,657] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:02,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:02,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014280965.1_ASM1428096v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:02,659] [INFO] Task started: Blastn
[2024-01-24 13:30:02,659] [INFO] Running command: blastn -query GCF_014280965.1_ASM1428096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae224068-baa4-41a9-8ea8-998a93e9569b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014280965.1_ASM1428096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:03,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:03,457] [INFO] Selected 12 target genomes.
[2024-01-24 13:30:03,457] [INFO] Target genome list was writen to GCF_014280965.1_ASM1428096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:03,469] [INFO] Task started: fastANI
[2024-01-24 13:30:03,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg6146d106-7e33-4bea-ae80-2142728863ec/GCF_014280965.1_ASM1428096v1_genomic.fna.gz --refList GCF_014280965.1_ASM1428096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014280965.1_ASM1428096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:15,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:15,980] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:15,980] [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	100.0	1699	1701	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018642165.1	s__Echinicola shivajiensis	85.3849	1362	1701	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	79.6615	621	1701	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	79.64	611	1701	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	77.9725	390	1701	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	77.609	402	1701	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	77.5257	296	1701	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000166275.1	s__Algoriphagus machipongonensis	76.6975	109	1701	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.5894	128	1701	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015476655.1	s__Aquiflexum lacus	76.4945	114	1701	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:15,983] [INFO] GTDB search result was written to GCF_014280965.1_ASM1428096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:15,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:15,988] [INFO] DFAST_QC result json was written to GCF_014280965.1_ASM1428096v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:15,988] [INFO] DFAST_QC completed!
[2024-01-24 13:30:15,988] [INFO] Total running time: 0h1m57s