[2024-01-25 19:47:20,417] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference
[2024-01-25 19:47:21,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,671] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84ab79a-ab43-4cb3-8652-16531e88e89c/GCF_000424665.1_ASM42466v1_genomic.fna.gz | prodigal -d GCF_000424665.1_ASM42466v1_genomic.fna/cds.fna -a GCF_000424665.1_ASM42466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:33,699] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:33,700] [INFO] Task started: HMMsearch
[2024-01-25 19:47:33,700] [INFO] Running command: hmmsearch --tblout GCF_000424665.1_ASM42466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/reference_markers.hmm GCF_000424665.1_ASM42466v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:34,023] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:34,026] [INFO] Found 6/6 markers.
[2024-01-25 19:47:34,056] [INFO] Query marker FASTA was written to GCF_000424665.1_ASM42466v1_genomic.fna/markers.fasta
[2024-01-25 19:47:34,057] [INFO] Task started: Blastn
[2024-01-25 19:47:34,057] [INFO] Running command: blastn -query GCF_000424665.1_ASM42466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/reference_markers.fasta -out GCF_000424665.1_ASM42466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:34,655] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:34,661] [INFO] Selected 15 target genomes.
[2024-01-25 19:47:34,661] [INFO] Target genome list was writen to GCF_000424665.1_ASM42466v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:34,697] [INFO] Task started: fastANI
[2024-01-25 19:47:34,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84ab79a-ab43-4cb3-8652-16531e88e89c/GCF_000424665.1_ASM42466v1_genomic.fna.gz --refList GCF_000424665.1_ASM42466v1_genomic.fna/target_genomes.txt --output GCF_000424665.1_ASM42466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:44,617] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:44,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:44,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:44,627] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:44,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:44,628] [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
Salinimicrobium terrae	strain=DSM 17865	GCA_000424665.1	470866	470866	type	True	100.0	1170	1170	95	conclusive
Salinimicrobium xinjiangense	strain=DSM 19287	GCA_000423585.1	438596	438596	type	True	79.5371	540	1170	95	below_threshold
Salinimicrobium oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	79.4162	429	1170	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	79.1443	485	1170	95	below_threshold
Salinimicrobium catena	strain=DSM 23553	GCA_900107495.1	390640	390640	type	True	77.9395	301	1170	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.9342	271	1170	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	77.9301	299	1170	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.435	163	1170	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	77.0022	132	1170	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	76.9835	131	1170	95	below_threshold
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	76.7605	100	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:44,629] [INFO] DFAST Taxonomy check result was written to GCF_000424665.1_ASM42466v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:44,630] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:44,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:44,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/checkm_data
[2024-01-25 19:47:44,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:44,669] [INFO] Task started: CheckM
[2024-01-25 19:47:44,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000424665.1_ASM42466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000424665.1_ASM42466v1_genomic.fna/checkm_input GCF_000424665.1_ASM42466v1_genomic.fna/checkm_result
[2024-01-25 19:48:22,330] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:22,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:22,346] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:22,347] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:22,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000424665.1_ASM42466v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:22,348] [INFO] Task started: Blastn
[2024-01-25 19:48:22,348] [INFO] Running command: blastn -query GCF_000424665.1_ASM42466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e5d8533-9486-462a-ad67-3cddf333fce1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000424665.1_ASM42466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:23,214] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:23,217] [INFO] Selected 10 target genomes.
[2024-01-25 19:48:23,217] [INFO] Target genome list was writen to GCF_000424665.1_ASM42466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:23,232] [INFO] Task started: fastANI
[2024-01-25 19:48:23,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84ab79a-ab43-4cb3-8652-16531e88e89c/GCF_000424665.1_ASM42466v1_genomic.fna.gz --refList GCF_000424665.1_ASM42466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000424665.1_ASM42466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:30,378] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:30,385] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:30,386] [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_000424665.1	s__Salinimicrobium terrae	100.0	1170	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423585.1	s__Salinimicrobium xinjiangense	79.5523	540	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	79.3609	484	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215295.1	s__Salinimicrobium sediminis	79.1345	486	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	77.9301	299	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651535.1	s__Salinimicrobium marinum	77.9214	272	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900095.1	s__Salegentibacter mishustinae	76.9835	131	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_009735585.1	s__Gramella aestuarii	76.9311	112	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001951155.1	s__Gramella flava	76.7365	100	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	-
GCF_000023465.1	s__Zunongwangia profunda	76.7201	110	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:30,387] [INFO] GTDB search result was written to GCF_000424665.1_ASM42466v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:30,387] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:30,390] [INFO] DFAST_QC result json was written to GCF_000424665.1_ASM42466v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:30,390] [INFO] DFAST_QC completed!
[2024-01-25 19:48:30,390] [INFO] Total running time: 0h1m10s