[2024-01-24 14:19:46,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference
[2024-01-24 14:19:48,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:48,177] [INFO] Task started: Prodigal
[2024-01-24 14:19:48,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3ab4777-e904-4bc7-b962-d9744a008409/GCF_003259255.1_ASM325925v1_genomic.fna.gz | prodigal -d GCF_003259255.1_ASM325925v1_genomic.fna/cds.fna -a GCF_003259255.1_ASM325925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:13,019] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:13,020] [INFO] Task started: HMMsearch
[2024-01-24 14:20:13,020] [INFO] Running command: hmmsearch --tblout GCF_003259255.1_ASM325925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/reference_markers.hmm GCF_003259255.1_ASM325925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:13,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:13,320] [INFO] Found 6/6 markers.
[2024-01-24 14:20:13,362] [INFO] Query marker FASTA was written to GCF_003259255.1_ASM325925v1_genomic.fna/markers.fasta
[2024-01-24 14:20:13,363] [INFO] Task started: Blastn
[2024-01-24 14:20:13,363] [INFO] Running command: blastn -query GCF_003259255.1_ASM325925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/reference_markers.fasta -out GCF_003259255.1_ASM325925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:14,018] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:14,022] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:14,022] [INFO] Target genome list was writen to GCF_003259255.1_ASM325925v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:14,034] [INFO] Task started: fastANI
[2024-01-24 14:20:14,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ab4777-e904-4bc7-b962-d9744a008409/GCF_003259255.1_ASM325925v1_genomic.fna.gz --refList GCF_003259255.1_ASM325925v1_genomic.fna/target_genomes.txt --output GCF_003259255.1_ASM325925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:25,940] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:25,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:25,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:25,949] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:25,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:25,950] [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 litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	100.0	1583	1586	95	conclusive
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	80.154	749	1586	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	79.1352	641	1586	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.5059	519	1586	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	78.1804	465	1586	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	78.1768	461	1586	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.9057	375	1586	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.0518	210	1586	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.958	235	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:25,952] [INFO] DFAST Taxonomy check result was written to GCF_003259255.1_ASM325925v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:25,952] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:25,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:25,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/checkm_data
[2024-01-24 14:20:25,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:25,999] [INFO] Task started: CheckM
[2024-01-24 14:20:26,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259255.1_ASM325925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259255.1_ASM325925v1_genomic.fna/checkm_input GCF_003259255.1_ASM325925v1_genomic.fna/checkm_result
[2024-01-24 14:21:34,310] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:34,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:34,332] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:34,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:34,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259255.1_ASM325925v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:34,333] [INFO] Task started: Blastn
[2024-01-24 14:21:34,334] [INFO] Running command: blastn -query GCF_003259255.1_ASM325925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e610184-dc87-4cc1-a2a4-851507cef971/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259255.1_ASM325925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:35,097] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:35,100] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:35,100] [INFO] Target genome list was writen to GCF_003259255.1_ASM325925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:35,114] [INFO] Task started: fastANI
[2024-01-24 14:21:35,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ab4777-e904-4bc7-b962-d9744a008409/GCF_003259255.1_ASM325925v1_genomic.fna.gz --refList GCF_003259255.1_ASM325925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259255.1_ASM325925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:44,124] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:44,133] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:44,133] [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_003259255.1	s__Algoriphagus litoralis	100.0	1583	1586	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_900108085.1	s__Algoriphagus boritolerans	80.1391	751	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	79.1351	641	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	78.5181	576	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	78.4934	520	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	78.1723	466	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	78.146	449	1586	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	78.0949	422	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	77.9	375	1586	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	77.0865	250	1586	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 14:21:44,134] [INFO] GTDB search result was written to GCF_003259255.1_ASM325925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:44,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:44,362] [INFO] DFAST_QC result json was written to GCF_003259255.1_ASM325925v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:44,363] [INFO] DFAST_QC completed!
[2024-01-24 14:21:44,363] [INFO] Total running time: 0h1m57s