[2024-01-24 12:21:40,325] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:40,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:40,328] [INFO] DQC Reference Directory: /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference
[2024-01-24 12:21:42,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:42,916] [INFO] Task started: Prodigal
[2024-01-24 12:21:42,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg04fa5881-ddf8-4867-8c58-4db794222961/GCF_000797445.1_ASM79744v1_genomic.fna.gz | prodigal -d GCF_000797445.1_ASM79744v1_genomic.fna/cds.fna -a GCF_000797445.1_ASM79744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:54,602] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:54,602] [INFO] Task started: HMMsearch
[2024-01-24 12:21:54,602] [INFO] Running command: hmmsearch --tblout GCF_000797445.1_ASM79744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/reference_markers.hmm GCF_000797445.1_ASM79744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:54,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:54,934] [INFO] Found 6/6 markers.
[2024-01-24 12:21:54,983] [INFO] Query marker FASTA was written to GCF_000797445.1_ASM79744v1_genomic.fna/markers.fasta
[2024-01-24 12:21:54,984] [INFO] Task started: Blastn
[2024-01-24 12:21:54,984] [INFO] Running command: blastn -query GCF_000797445.1_ASM79744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/reference_markers.fasta -out GCF_000797445.1_ASM79744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:55,704] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:55,713] [INFO] Selected 19 target genomes.
[2024-01-24 12:21:55,713] [INFO] Target genome list was writen to GCF_000797445.1_ASM79744v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:55,720] [INFO] Task started: fastANI
[2024-01-24 12:21:55,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg04fa5881-ddf8-4867-8c58-4db794222961/GCF_000797445.1_ASM79744v1_genomic.fna.gz --refList GCF_000797445.1_ASM79744v1_genomic.fna/target_genomes.txt --output GCF_000797445.1_ASM79744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:10,053] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:10,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:10,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:10,069] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:10,069] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:10,069] [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
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	100.0	1304	1314	95	conclusive
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	82.4614	747	1314	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	82.2577	732	1314	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.6909	448	1314	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	78.545	388	1314	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.427	405	1314	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	78.2023	412	1314	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.1207	335	1314	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	78.1085	328	1314	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.0001	325	1314	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.9628	288	1314	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.8657	309	1314	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.8561	302	1314	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.8403	306	1314	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6508	237	1314	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2439	253	1314	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.1935	213	1314	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.0796	155	1314	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0492	182	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:10,071] [INFO] DFAST Taxonomy check result was written to GCF_000797445.1_ASM79744v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:10,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:10,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:10,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/checkm_data
[2024-01-24 12:22:10,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:10,120] [INFO] Task started: CheckM
[2024-01-24 12:22:10,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000797445.1_ASM79744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000797445.1_ASM79744v1_genomic.fna/checkm_input GCF_000797445.1_ASM79744v1_genomic.fna/checkm_result
[2024-01-24 12:22:47,924] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:47,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,959] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:47,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:47,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000797445.1_ASM79744v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:47,961] [INFO] Task started: Blastn
[2024-01-24 12:22:47,961] [INFO] Running command: blastn -query GCF_000797445.1_ASM79744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb049efd1-408f-40fc-bd65-fbb5220120bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000797445.1_ASM79744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:49,117] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:49,126] [INFO] Selected 7 target genomes.
[2024-01-24 12:22:49,126] [INFO] Target genome list was writen to GCF_000797445.1_ASM79744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:49,137] [INFO] Task started: fastANI
[2024-01-24 12:22:49,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg04fa5881-ddf8-4867-8c58-4db794222961/GCF_000797445.1_ASM79744v1_genomic.fna.gz --refList GCF_000797445.1_ASM79744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000797445.1_ASM79744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:55,130] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:55,142] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:55,142] [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_000797445.1	s__Lacinutrix jangbogonensis	100.0	1304	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002831665.1	s__Lacinutrix sp002831665	83.3416	801	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	82.4795	745	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	82.2092	737	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	80.8197	627	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	79.7829	516	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	79.7164	512	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,145] [INFO] GTDB search result was written to GCF_000797445.1_ASM79744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:55,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:55,152] [INFO] DFAST_QC result json was written to GCF_000797445.1_ASM79744v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:55,153] [INFO] DFAST_QC completed!
[2024-01-24 12:22:55,153] [INFO] Total running time: 0h1m15s