[2024-01-24 14:02:49,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:49,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:49,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference
[2024-01-24 14:02:50,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:50,499] [INFO] Task started: Prodigal
[2024-01-24 14:02:50,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cae9e72-47ff-42cd-92f0-452b2c50edc7/GCF_000148645.1_ASM14864v1_genomic.fna.gz | prodigal -d GCF_000148645.1_ASM14864v1_genomic.fna/cds.fna -a GCF_000148645.1_ASM14864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:04,467] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:04,468] [INFO] Task started: HMMsearch
[2024-01-24 14:03:04,468] [INFO] Running command: hmmsearch --tblout GCF_000148645.1_ASM14864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/reference_markers.hmm GCF_000148645.1_ASM14864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:04,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:04,776] [INFO] Found 6/6 markers.
[2024-01-24 14:03:04,814] [INFO] Query marker FASTA was written to GCF_000148645.1_ASM14864v1_genomic.fna/markers.fasta
[2024-01-24 14:03:04,814] [INFO] Task started: Blastn
[2024-01-24 14:03:04,814] [INFO] Running command: blastn -query GCF_000148645.1_ASM14864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/reference_markers.fasta -out GCF_000148645.1_ASM14864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:05,767] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:05,770] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:05,770] [INFO] Target genome list was writen to GCF_000148645.1_ASM14864v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:05,777] [INFO] Task started: fastANI
[2024-01-24 14:03:05,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cae9e72-47ff-42cd-92f0-452b2c50edc7/GCF_000148645.1_ASM14864v1_genomic.fna.gz --refList GCF_000148645.1_ASM14864v1_genomic.fna/target_genomes.txt --output GCF_000148645.1_ASM14864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:16,731] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:16,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:16,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:16,746] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:16,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:16,747] [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
Ferrimonas balearica	strain=DSM 9799	GCA_000148645.1	44012	44012	type	True	100.0	1425	1426	95	conclusive
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	80.0595	684	1426	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	80.0409	659	1426	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	78.9276	443	1426	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	78.7551	445	1426	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	78.161	406	1426	95	below_threshold
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	78.0651	399	1426	95	below_threshold
Ferrimonas senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	77.9542	313	1426	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.0388	149	1426	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	76.8184	90	1426	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.5399	124	1426	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.5112	105	1426	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.5083	118	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:16,748] [INFO] DFAST Taxonomy check result was written to GCF_000148645.1_ASM14864v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:16,749] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:16,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:16,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/checkm_data
[2024-01-24 14:03:16,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:16,798] [INFO] Task started: CheckM
[2024-01-24 14:03:16,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000148645.1_ASM14864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000148645.1_ASM14864v1_genomic.fna/checkm_input GCF_000148645.1_ASM14864v1_genomic.fna/checkm_result
[2024-01-24 14:03:57,920] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:57,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:57,942] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:57,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:57,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000148645.1_ASM14864v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:57,943] [INFO] Task started: Blastn
[2024-01-24 14:03:57,943] [INFO] Running command: blastn -query GCF_000148645.1_ASM14864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f1e02e5-c512-4f8e-bc4d-2fdf9e73241f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000148645.1_ASM14864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:59,425] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:59,429] [INFO] Selected 9 target genomes.
[2024-01-24 14:03:59,429] [INFO] Target genome list was writen to GCF_000148645.1_ASM14864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:59,436] [INFO] Task started: fastANI
[2024-01-24 14:03:59,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cae9e72-47ff-42cd-92f0-452b2c50edc7/GCF_000148645.1_ASM14864v1_genomic.fna.gz --refList GCF_000148645.1_ASM14864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000148645.1_ASM14864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:07,155] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:07,171] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:07,171] [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_000148645.1	s__Ferrimonas balearica	100.0	1425	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129905.1	s__Ferrimonas marina	80.0513	685	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005116715.1	s__Ferrimonas sp005116715	78.9193	444	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	78.7307	447	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100175.1	s__Ferrimonas sediminum	78.1485	407	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	78.0937	398	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422665.1	s__Ferrimonas senticii	77.9533	313	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	77.2025	177	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002936955.1	s__Oceanisphaera arctica	77.074	153	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:07,173] [INFO] GTDB search result was written to GCF_000148645.1_ASM14864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:07,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:07,179] [INFO] DFAST_QC result json was written to GCF_000148645.1_ASM14864v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:07,179] [INFO] DFAST_QC completed!
[2024-01-24 14:04:07,179] [INFO] Total running time: 0h1m18s