[2024-01-24 14:06:05,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference
[2024-01-24 14:06:06,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:06,963] [INFO] Task started: Prodigal
[2024-01-24 14:06:06,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgb30d4fe2-60f0-407e-8d1d-239e5cfab089/GCF_018642165.1_ASM1864216v1_genomic.fna.gz | prodigal -d GCF_018642165.1_ASM1864216v1_genomic.fna/cds.fna -a GCF_018642165.1_ASM1864216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:32,755] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:32,756] [INFO] Task started: HMMsearch
[2024-01-24 14:06:32,756] [INFO] Running command: hmmsearch --tblout GCF_018642165.1_ASM1864216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/reference_markers.hmm GCF_018642165.1_ASM1864216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:33,093] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:33,095] [INFO] Found 6/6 markers.
[2024-01-24 14:06:33,149] [INFO] Query marker FASTA was written to GCF_018642165.1_ASM1864216v1_genomic.fna/markers.fasta
[2024-01-24 14:06:33,150] [INFO] Task started: Blastn
[2024-01-24 14:06:33,150] [INFO] Running command: blastn -query GCF_018642165.1_ASM1864216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/reference_markers.fasta -out GCF_018642165.1_ASM1864216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:33,805] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:33,811] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:33,812] [INFO] Target genome list was writen to GCF_018642165.1_ASM1864216v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:33,822] [INFO] Task started: fastANI
[2024-01-24 14:06:33,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgb30d4fe2-60f0-407e-8d1d-239e5cfab089/GCF_018642165.1_ASM1864216v1_genomic.fna.gz --refList GCF_018642165.1_ASM1864216v1_genomic.fna/target_genomes.txt --output GCF_018642165.1_ASM1864216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:47,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:47,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:47,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:47,433] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:47,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:47,433] [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 shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	100.0	1861	1863	95	conclusive
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	85.3834	1369	1863	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	85.0363	1265	1863	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	80.1589	681	1863	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	78.3265	369	1863	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	78.0294	377	1863	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	77.4526	285	1863	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.9378	110	1863	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	76.6311	147	1863	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.6185	116	1863	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	76.4831	119	1863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:47,435] [INFO] DFAST Taxonomy check result was written to GCF_018642165.1_ASM1864216v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:47,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:47,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:47,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/checkm_data
[2024-01-24 14:06:47,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:47,492] [INFO] Task started: CheckM
[2024-01-24 14:06:47,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018642165.1_ASM1864216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018642165.1_ASM1864216v1_genomic.fna/checkm_input GCF_018642165.1_ASM1864216v1_genomic.fna/checkm_result
[2024-01-24 14:07:57,798] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:57,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:57,818] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:57,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:57,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018642165.1_ASM1864216v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:57,820] [INFO] Task started: Blastn
[2024-01-24 14:07:57,820] [INFO] Running command: blastn -query GCF_018642165.1_ASM1864216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96601e2-22dd-41a4-ae08-dea226eef3cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_018642165.1_ASM1864216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:58,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:58,650] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:58,650] [INFO] Target genome list was writen to GCF_018642165.1_ASM1864216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:58,668] [INFO] Task started: fastANI
[2024-01-24 14:07:58,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgb30d4fe2-60f0-407e-8d1d-239e5cfab089/GCF_018642165.1_ASM1864216v1_genomic.fna.gz --refList GCF_018642165.1_ASM1864216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018642165.1_ASM1864216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:13,447] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:13,465] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:13,466] [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_018642165.1	s__Echinicola shivajiensis	100.0	1861	1863	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_014280965.1	s__Echinicola sp014280965	85.3906	1367	1863	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	80.1426	684	1863	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	79.8841	686	1863	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	78.3265	369	1863	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	78.2268	382	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281475.1	s__Echinicola rosea	78.225	377	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003260975.1	s__Echinicola strongylocentroti	78.0384	375	1863	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	77.4334	285	1863	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	76.9378	110	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.8009	118	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206875.1	s__Algoriphagus iocasae	76.6463	146	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	76.5829	116	1863	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.4733	120	1863	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 14:08:13,467] [INFO] GTDB search result was written to GCF_018642165.1_ASM1864216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:13,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:13,471] [INFO] DFAST_QC result json was written to GCF_018642165.1_ASM1864216v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:13,471] [INFO] DFAST_QC completed!
[2024-01-24 14:08:13,471] [INFO] Total running time: 0h2m8s