[2024-01-24 13:28:26,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:26,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:26,204] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference
[2024-01-24 13:28:27,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,616] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeb7cdf1-fac0-46d5-b810-69a635228e1d/GCF_000422665.1_ASM42266v1_genomic.fna.gz | prodigal -d GCF_000422665.1_ASM42266v1_genomic.fna/cds.fna -a GCF_000422665.1_ASM42266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:39,897] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:39,897] [INFO] Task started: HMMsearch
[2024-01-24 13:28:39,898] [INFO] Running command: hmmsearch --tblout GCF_000422665.1_ASM42266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/reference_markers.hmm GCF_000422665.1_ASM42266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:40,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:40,244] [INFO] Found 6/6 markers.
[2024-01-24 13:28:40,280] [INFO] Query marker FASTA was written to GCF_000422665.1_ASM42266v1_genomic.fna/markers.fasta
[2024-01-24 13:28:40,281] [INFO] Task started: Blastn
[2024-01-24 13:28:40,281] [INFO] Running command: blastn -query GCF_000422665.1_ASM42266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/reference_markers.fasta -out GCF_000422665.1_ASM42266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:41,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:41,237] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:41,237] [INFO] Target genome list was writen to GCF_000422665.1_ASM42266v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:41,256] [INFO] Task started: fastANI
[2024-01-24 13:28:41,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb7cdf1-fac0-46d5-b810-69a635228e1d/GCF_000422665.1_ASM42266v1_genomic.fna.gz --refList GCF_000422665.1_ASM42266v1_genomic.fna/target_genomes.txt --output GCF_000422665.1_ASM42266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:52,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:52,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:52,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:52,961] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:52,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:52,961] [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 senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	100.0	1276	1278	95	conclusive
Ferrimonas lipolytica	strain=S7	GCA_012295575.1	2724191	2724191	type	True	78.4673	321	1278	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	77.9801	263	1278	95	below_threshold
Ferrimonas balearica	strain=DSM 9799	GCA_000148645.1	44012	44012	type	True	77.9036	308	1278	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	77.8759	256	1278	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	77.3409	175	1278	95	below_threshold
Vibrio proteolyticus	strain=NBRC 13287	GCA_000467125.1	671	671	type	True	76.5714	59	1278	95	below_threshold
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	76.2845	67	1278	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.7848	50	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:52,963] [INFO] DFAST Taxonomy check result was written to GCF_000422665.1_ASM42266v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:52,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:52,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:52,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/checkm_data
[2024-01-24 13:28:52,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:53,008] [INFO] Task started: CheckM
[2024-01-24 13:28:53,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422665.1_ASM42266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422665.1_ASM42266v1_genomic.fna/checkm_input GCF_000422665.1_ASM42266v1_genomic.fna/checkm_result
[2024-01-24 13:29:31,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:31,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:31,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:31,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:31,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422665.1_ASM42266v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:31,257] [INFO] Task started: Blastn
[2024-01-24 13:29:31,257] [INFO] Running command: blastn -query GCF_000422665.1_ASM42266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a48ee9-3cb9-43f4-89c4-afeebb155f6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422665.1_ASM42266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:32,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:32,734] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:32,734] [INFO] Target genome list was writen to GCF_000422665.1_ASM42266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:32,759] [INFO] Task started: fastANI
[2024-01-24 13:29:32,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb7cdf1-fac0-46d5-b810-69a635228e1d/GCF_000422665.1_ASM42266v1_genomic.fna.gz --refList GCF_000422665.1_ASM42266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422665.1_ASM42266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:44,594] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:44,609] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:44,609] [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_000422665.1	s__Ferrimonas senticii	100.0	1276	1278	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_012295575.1	s__Ferrimonas lipolytica	78.4608	322	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129905.1	s__Ferrimonas marina	77.9787	263	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000148645.1	s__Ferrimonas balearica	77.9073	307	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116665.1	s__Ferrimonas sp005116665	77.8507	209	1278	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	77.3277	175	1278	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	77.2367	208	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467125.1	s__Vibrio proteolyticus	76.5714	59	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_900637545.1	s__Aeromonas encheleia	76.3318	93	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_017354945.1	s__Shewanella sp017354945	76.2609	68	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	75.6894	53	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:44,615] [INFO] GTDB search result was written to GCF_000422665.1_ASM42266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:44,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:44,625] [INFO] DFAST_QC result json was written to GCF_000422665.1_ASM42266v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:44,626] [INFO] DFAST_QC completed!
[2024-01-24 13:29:44,626] [INFO] Total running time: 0h1m18s