[2024-01-24 13:17:15,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,648] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference
[2024-01-24 13:17:17,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,020] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg376a31e7-bfa7-4b1c-80ff-754f6288fb49/GCF_001975705.1_ASM197570v1_genomic.fna.gz | prodigal -d GCF_001975705.1_ASM197570v1_genomic.fna/cds.fna -a GCF_001975705.1_ASM197570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,307] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,307] [INFO] Running command: hmmsearch --tblout GCF_001975705.1_ASM197570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/reference_markers.hmm GCF_001975705.1_ASM197570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,636] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,683] [INFO] Query marker FASTA was written to GCF_001975705.1_ASM197570v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,683] [INFO] Task started: Blastn
[2024-01-24 13:17:33,684] [INFO] Running command: blastn -query GCF_001975705.1_ASM197570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/reference_markers.fasta -out GCF_001975705.1_ASM197570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,705] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:34,705] [INFO] Target genome list was writen to GCF_001975705.1_ASM197570v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,709] [INFO] Task started: fastANI
[2024-01-24 13:17:34,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg376a31e7-bfa7-4b1c-80ff-754f6288fb49/GCF_001975705.1_ASM197570v1_genomic.fna.gz --refList GCF_001975705.1_ASM197570v1_genomic.fna/target_genomes.txt --output GCF_001975705.1_ASM197570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:47,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:47,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:47,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:47,859] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:47,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:47,860] [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
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	84.031	1022	1748	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	83.5435	1015	1748	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	83.4512	1037	1748	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	83.3885	1003	1748	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	81.4301	859	1748	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	81.2076	867	1748	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	81.1987	857	1748	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	81.0492	827	1748	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.5897	776	1748	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.8774	532	1748	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.6306	571	1748	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.8221	412	1748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:47,861] [INFO] DFAST Taxonomy check result was written to GCF_001975705.1_ASM197570v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:47,862] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:47,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:47,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/checkm_data
[2024-01-24 13:17:47,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:47,912] [INFO] Task started: CheckM
[2024-01-24 13:17:47,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001975705.1_ASM197570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001975705.1_ASM197570v1_genomic.fna/checkm_input GCF_001975705.1_ASM197570v1_genomic.fna/checkm_result
[2024-01-24 13:18:41,949] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:41,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:41,972] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:41,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:41,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001975705.1_ASM197570v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:41,973] [INFO] Task started: Blastn
[2024-01-24 13:18:41,973] [INFO] Running command: blastn -query GCF_001975705.1_ASM197570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf675476-e6c0-4349-95e7-39e665cff7e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001975705.1_ASM197570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:43,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:43,754] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:43,755] [INFO] Target genome list was writen to GCF_001975705.1_ASM197570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:43,767] [INFO] Task started: fastANI
[2024-01-24 13:18:43,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg376a31e7-bfa7-4b1c-80ff-754f6288fb49/GCF_001975705.1_ASM197570v1_genomic.fna.gz --refList GCF_001975705.1_ASM197570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001975705.1_ASM197570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:54,940] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:54,952] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:54,952] [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_001975705.1	s__Salipiger abyssi	100.0	1748	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017311415.1	s__Salipiger abyssi_A	94.8204	1319	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	84.0269	1021	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900102075.1	s__Salipiger thiooxidans	83.53	1017	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_001969385.1	s__Salipiger profundus	83.4649	1032	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_000442255.1	s__Salipiger mucosus	81.9894	878	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	81.3998	864	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_900116195.1	s__Salipiger pacificus	81.2188	865	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000813985.1	s__Ruegeria sp000813985	77.1701	281	1748	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,953] [INFO] GTDB search result was written to GCF_001975705.1_ASM197570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:54,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:54,957] [INFO] DFAST_QC result json was written to GCF_001975705.1_ASM197570v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:54,957] [INFO] DFAST_QC completed!
[2024-01-24 13:18:54,957] [INFO] Total running time: 0h1m39s