[2024-01-25 17:35:35,381] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference
[2024-01-25 17:35:36,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,524] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f1e9b93-a701-4339-89ff-3698228e2cc0/GCF_016464625.1_ASM1646462v1_genomic.fna.gz | prodigal -d GCF_016464625.1_ASM1646462v1_genomic.fna/cds.fna -a GCF_016464625.1_ASM1646462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:46,970] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:46,970] [INFO] Task started: HMMsearch
[2024-01-25 17:35:46,970] [INFO] Running command: hmmsearch --tblout GCF_016464625.1_ASM1646462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/reference_markers.hmm GCF_016464625.1_ASM1646462v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:47,176] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:47,177] [INFO] Found 6/6 markers.
[2024-01-25 17:35:47,201] [INFO] Query marker FASTA was written to GCF_016464625.1_ASM1646462v1_genomic.fna/markers.fasta
[2024-01-25 17:35:47,201] [INFO] Task started: Blastn
[2024-01-25 17:35:47,201] [INFO] Running command: blastn -query GCF_016464625.1_ASM1646462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/reference_markers.fasta -out GCF_016464625.1_ASM1646462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:47,757] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:47,760] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:47,760] [INFO] Target genome list was writen to GCF_016464625.1_ASM1646462v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:47,805] [INFO] Task started: fastANI
[2024-01-25 17:35:47,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f1e9b93-a701-4339-89ff-3698228e2cc0/GCF_016464625.1_ASM1646462v1_genomic.fna.gz --refList GCF_016464625.1_ASM1646462v1_genomic.fna/target_genomes.txt --output GCF_016464625.1_ASM1646462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:03,323] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:03,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:03,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:03,330] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:03,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:03,330] [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
Penaeicola halotolerans	strain=LMIT005	GCA_016464625.1	2793196	2793196	type	True	100.0	1000	1001	95	conclusive
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	77.0976	57	1001	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.8573	53	1001	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	76.4129	52	1001	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	76.2884	59	1001	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.2884	59	1001	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.1356	51	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:03,331] [INFO] DFAST Taxonomy check result was written to GCF_016464625.1_ASM1646462v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:03,332] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:03,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:03,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/checkm_data
[2024-01-25 17:36:03,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:03,367] [INFO] Task started: CheckM
[2024-01-25 17:36:03,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464625.1_ASM1646462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464625.1_ASM1646462v1_genomic.fna/checkm_input GCF_016464625.1_ASM1646462v1_genomic.fna/checkm_result
[2024-01-25 17:36:37,607] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:37,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:37,663] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:37,663] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:37,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464625.1_ASM1646462v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:37,664] [INFO] Task started: Blastn
[2024-01-25 17:36:37,664] [INFO] Running command: blastn -query GCF_016464625.1_ASM1646462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8591b3dc-5e55-44f7-b9bd-dcb4de58b135/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464625.1_ASM1646462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:38,551] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:38,555] [INFO] Selected 25 target genomes.
[2024-01-25 17:36:38,555] [INFO] Target genome list was writen to GCF_016464625.1_ASM1646462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:38,568] [INFO] Task started: fastANI
[2024-01-25 17:36:38,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f1e9b93-a701-4339-89ff-3698228e2cc0/GCF_016464625.1_ASM1646462v1_genomic.fna.gz --refList GCF_016464625.1_ASM1646462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464625.1_ASM1646462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:56,240] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:56,248] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:56,248] [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_016464625.1	s__LMIT005 sp016464625	100.0	1000	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__LMIT005	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018642165.1	s__Echinicola shivajiensis	77.1497	55	1001	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	76.9023	52	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	76.8284	52	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_014841125.1	s__Echinicola sp014841125	76.4501	51	1001	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	76.4055	53	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.2884	59	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.1356	51	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	76.0755	50	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:56,249] [INFO] GTDB search result was written to GCF_016464625.1_ASM1646462v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:56,250] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:56,253] [INFO] DFAST_QC result json was written to GCF_016464625.1_ASM1646462v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:56,253] [INFO] DFAST_QC completed!
[2024-01-25 17:36:56,253] [INFO] Total running time: 0h1m21s