[2024-01-24 13:01:52,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:52,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:52,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference
[2024-01-24 13:01:53,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:53,893] [INFO] Task started: Prodigal
[2024-01-24 13:01:53,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a4252b2-535b-4824-8cb7-789b82d891c7/GCF_007655305.1_ASM765530v1_genomic.fna.gz | prodigal -d GCF_007655305.1_ASM765530v1_genomic.fna/cds.fna -a GCF_007655305.1_ASM765530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:12,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:12,963] [INFO] Task started: HMMsearch
[2024-01-24 13:02:12,963] [INFO] Running command: hmmsearch --tblout GCF_007655305.1_ASM765530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/reference_markers.hmm GCF_007655305.1_ASM765530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:13,323] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:13,324] [INFO] Found 6/6 markers.
[2024-01-24 13:02:13,367] [INFO] Query marker FASTA was written to GCF_007655305.1_ASM765530v1_genomic.fna/markers.fasta
[2024-01-24 13:02:13,368] [INFO] Task started: Blastn
[2024-01-24 13:02:13,368] [INFO] Running command: blastn -query GCF_007655305.1_ASM765530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/reference_markers.fasta -out GCF_007655305.1_ASM765530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:13,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:13,969] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:13,969] [INFO] Target genome list was writen to GCF_007655305.1_ASM765530v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:13,974] [INFO] Task started: fastANI
[2024-01-24 13:02:13,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a4252b2-535b-4824-8cb7-789b82d891c7/GCF_007655305.1_ASM765530v1_genomic.fna.gz --refList GCF_007655305.1_ASM765530v1_genomic.fna/target_genomes.txt --output GCF_007655305.1_ASM765530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:25,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:25,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:25,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:25,948] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:25,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:25,948] [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
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	100.0	1448	1449	95	conclusive
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	94.4746	1196	1449	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	78.9049	312	1449	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	78.789	400	1449	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	78.708	404	1449	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	78.2871	344	1449	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	77.4667	209	1449	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.0941	227	1449	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	77.0907	224	1449	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	77.0581	220	1449	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.438	65	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:25,950] [INFO] DFAST Taxonomy check result was written to GCF_007655305.1_ASM765530v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:25,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:25,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:25,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/checkm_data
[2024-01-24 13:02:25,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:25,997] [INFO] Task started: CheckM
[2024-01-24 13:02:25,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007655305.1_ASM765530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007655305.1_ASM765530v1_genomic.fna/checkm_input GCF_007655305.1_ASM765530v1_genomic.fna/checkm_result
[2024-01-24 13:03:23,694] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:23,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:23,723] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:23,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:23,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007655305.1_ASM765530v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:23,725] [INFO] Task started: Blastn
[2024-01-24 13:03:23,725] [INFO] Running command: blastn -query GCF_007655305.1_ASM765530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eaaa06a-198f-4815-8df5-9ce3a2bdb25e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007655305.1_ASM765530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:24,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:24,579] [INFO] Selected 15 target genomes.
[2024-01-24 13:03:24,579] [INFO] Target genome list was writen to GCF_007655305.1_ASM765530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:24,588] [INFO] Task started: fastANI
[2024-01-24 13:03:24,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a4252b2-535b-4824-8cb7-789b82d891c7/GCF_007655305.1_ASM765530v1_genomic.fna.gz --refList GCF_007655305.1_ASM765530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007655305.1_ASM765530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:38,042] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:38,059] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:38,060] [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_007655305.1	s__Algoriphagus sp007655305	100.0	1448	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115305.1	s__Algoriphagus ornithinivorans	94.4746	1196	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_014206875.1	s__Algoriphagus iocasae	78.9193	311	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	78.8722	355	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	78.7852	399	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429465.1	s__Algoriphagus vanfongensis	78.2871	344	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	78.0324	382	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	77.7909	220	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373335.1	s__Algoriphagus sp013373335	77.702	240	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.6809	281	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	77.6266	251	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	77.4667	209	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	77.3899	221	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	77.0581	220	1449	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	76.5367	118	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:38,079] [INFO] GTDB search result was written to GCF_007655305.1_ASM765530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:38,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:38,087] [INFO] DFAST_QC result json was written to GCF_007655305.1_ASM765530v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:38,088] [INFO] DFAST_QC completed!
[2024-01-24 13:03:38,088] [INFO] Total running time: 0h1m46s