[2024-01-24 14:12:47,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference
[2024-01-24 14:12:48,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,332] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,332] [INFO] Running command: gunzip -c /var/lib/cwl/stg27a1c7a7-92e0-4efe-9454-4315c57bdc04/GCF_014841125.1_ASM1484112v1_genomic.fna.gz | prodigal -d GCF_014841125.1_ASM1484112v1_genomic.fna/cds.fna -a GCF_014841125.1_ASM1484112v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:13,892] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:13,893] [INFO] Task started: HMMsearch
[2024-01-24 14:13:13,893] [INFO] Running command: hmmsearch --tblout GCF_014841125.1_ASM1484112v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/reference_markers.hmm GCF_014841125.1_ASM1484112v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:14,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:14,201] [INFO] Found 6/6 markers.
[2024-01-24 14:13:14,248] [INFO] Query marker FASTA was written to GCF_014841125.1_ASM1484112v1_genomic.fna/markers.fasta
[2024-01-24 14:13:14,249] [INFO] Task started: Blastn
[2024-01-24 14:13:14,249] [INFO] Running command: blastn -query GCF_014841125.1_ASM1484112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/reference_markers.fasta -out GCF_014841125.1_ASM1484112v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:14,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:14,870] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:14,870] [INFO] Target genome list was writen to GCF_014841125.1_ASM1484112v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:14,885] [INFO] Task started: fastANI
[2024-01-24 14:13:14,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a1c7a7-92e0-4efe-9454-4315c57bdc04/GCF_014841125.1_ASM1484112v1_genomic.fna.gz --refList GCF_014841125.1_ASM1484112v1_genomic.fna/target_genomes.txt --output GCF_014841125.1_ASM1484112v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:29,284] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:29,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:29,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:29,295] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:29,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:29,295] [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 arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	100.0	1784	1784	95	conclusive
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	80.0617	693	1784	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	79.7973	624	1784	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	79.5539	620	1784	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	78.4681	476	1784	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	78.2401	438	1784	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	77.6955	298	1784	95	below_threshold
Echinicola pacifica	strain=DSM 19836	GCA_000373245.1	346377	346377	type	True	77.6852	299	1784	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.8419	120	1784	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.8114	95	1784	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.6024	115	1784	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.3778	72	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:29,297] [INFO] DFAST Taxonomy check result was written to GCF_014841125.1_ASM1484112v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:29,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:29,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:29,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/checkm_data
[2024-01-24 14:13:29,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:29,349] [INFO] Task started: CheckM
[2024-01-24 14:13:29,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841125.1_ASM1484112v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841125.1_ASM1484112v1_genomic.fna/checkm_input GCF_014841125.1_ASM1484112v1_genomic.fna/checkm_result
[2024-01-24 14:14:42,664] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:42,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,689] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:42,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:42,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841125.1_ASM1484112v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:42,690] [INFO] Task started: Blastn
[2024-01-24 14:14:42,690] [INFO] Running command: blastn -query GCF_014841125.1_ASM1484112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296aff62-a6a0-4652-8f0f-32137ee5542c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841125.1_ASM1484112v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:43,460] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:43,463] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:43,464] [INFO] Target genome list was writen to GCF_014841125.1_ASM1484112v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:43,475] [INFO] Task started: fastANI
[2024-01-24 14:14:43,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a1c7a7-92e0-4efe-9454-4315c57bdc04/GCF_014841125.1_ASM1484112v1_genomic.fna.gz --refList GCF_014841125.1_ASM1484112v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841125.1_ASM1484112v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:54,293] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:54,304] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:54,305] [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_014841125.1	s__Echinicola sp014841125	100.0	1784	1784	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_015533855.1	s__Echinicola sp015533855	92.3277	1533	1784	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	80.0673	693	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	79.5442	622	1784	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	78.4566	478	1784	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	78.2493	437	1784	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	77.6744	300	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004216715.1	s__Cecembia calidifontis	76.8419	120	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.6024	115	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	76.3332	83	1784	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 14:14:54,306] [INFO] GTDB search result was written to GCF_014841125.1_ASM1484112v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:54,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:54,309] [INFO] DFAST_QC result json was written to GCF_014841125.1_ASM1484112v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:54,309] [INFO] DFAST_QC completed!
[2024-01-24 14:14:54,310] [INFO] Total running time: 0h2m7s