[2024-01-25 17:46:20,791] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,793] [INFO] DQC Reference Directory: /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference
[2024-01-25 17:46:21,985] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,986] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,986] [INFO] Running command: gunzip -c /var/lib/cwl/stg87c0d0ef-f11d-4506-8abf-03a57ebce855/GCF_014643635.1_ASM1464363v1_genomic.fna.gz | prodigal -d GCF_014643635.1_ASM1464363v1_genomic.fna/cds.fna -a GCF_014643635.1_ASM1464363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:34,403] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:34,403] [INFO] Task started: HMMsearch
[2024-01-25 17:46:34,403] [INFO] Running command: hmmsearch --tblout GCF_014643635.1_ASM1464363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/reference_markers.hmm GCF_014643635.1_ASM1464363v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:34,635] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:34,636] [INFO] Found 6/6 markers.
[2024-01-25 17:46:34,672] [INFO] Query marker FASTA was written to GCF_014643635.1_ASM1464363v1_genomic.fna/markers.fasta
[2024-01-25 17:46:34,673] [INFO] Task started: Blastn
[2024-01-25 17:46:34,673] [INFO] Running command: blastn -query GCF_014643635.1_ASM1464363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/reference_markers.fasta -out GCF_014643635.1_ASM1464363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:35,651] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:35,653] [INFO] Selected 13 target genomes.
[2024-01-25 17:46:35,654] [INFO] Target genome list was writen to GCF_014643635.1_ASM1464363v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:35,659] [INFO] Task started: fastANI
[2024-01-25 17:46:35,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c0d0ef-f11d-4506-8abf-03a57ebce855/GCF_014643635.1_ASM1464363v1_genomic.fna.gz --refList GCF_014643635.1_ASM1464363v1_genomic.fna/target_genomes.txt --output GCF_014643635.1_ASM1464363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:48,400] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:48,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:48,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:48,410] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:48,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:48,410] [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 pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	100.0	1471	1472	95	conclusive
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	82.3884	891	1472	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	82.337	869	1472	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	82.1574	897	1472	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	81.8779	906	1472	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	80.5423	751	1472	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	80.5004	757	1472	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.0258	673	1472	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	79.9882	674	1472	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.7157	670	1472	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.9443	450	1472	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6245	367	1472	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.5567	309	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:48,412] [INFO] DFAST Taxonomy check result was written to GCF_014643635.1_ASM1464363v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:48,412] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:48,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:48,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/checkm_data
[2024-01-25 17:46:48,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:48,457] [INFO] Task started: CheckM
[2024-01-25 17:46:48,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643635.1_ASM1464363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643635.1_ASM1464363v1_genomic.fna/checkm_input GCF_014643635.1_ASM1464363v1_genomic.fna/checkm_result
[2024-01-25 17:47:29,301] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:29,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:29,317] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:29,317] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:29,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643635.1_ASM1464363v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:29,318] [INFO] Task started: Blastn
[2024-01-25 17:47:29,318] [INFO] Running command: blastn -query GCF_014643635.1_ASM1464363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf133f137-28a0-4297-a570-9dd70acea3d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643635.1_ASM1464363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:31,101] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:31,104] [INFO] Selected 13 target genomes.
[2024-01-25 17:47:31,104] [INFO] Target genome list was writen to GCF_014643635.1_ASM1464363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:31,115] [INFO] Task started: fastANI
[2024-01-25 17:47:31,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c0d0ef-f11d-4506-8abf-03a57ebce855/GCF_014643635.1_ASM1464363v1_genomic.fna.gz --refList GCF_014643635.1_ASM1464363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643635.1_ASM1464363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:46,484] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:46,493] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:46,494] [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_014643635.1	s__Salipiger pallidus	100.0	1471	1472	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_001969385.1	s__Salipiger profundus	82.3847	891	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900102075.1	s__Salipiger thiooxidans	82.1381	901	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000153725.1	s__Salipiger bermudensis	81.8609	909	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_017311415.1	s__Salipiger abyssi_A	81.3322	798	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	81.2017	811	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	80.7489	557	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	80.5376	752	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018860705.1	s__Salipiger sp018860705	80.5158	758	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	80.4103	747	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	80.3864	742	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	80.3571	732	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_001687105.1	s__Salipiger sp001687105	80.2849	730	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:46,496] [INFO] GTDB search result was written to GCF_014643635.1_ASM1464363v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:46,496] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:46,499] [INFO] DFAST_QC result json was written to GCF_014643635.1_ASM1464363v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:46,500] [INFO] DFAST_QC completed!
[2024-01-25 17:47:46,500] [INFO] Total running time: 0h1m26s