[2024-01-24 12:06:13,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference
[2024-01-24 12:06:15,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,310] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,310] [INFO] Running command: gunzip -c /var/lib/cwl/stgaccc7d23-debe-4133-8a7c-6bf6e75b29dd/GCF_015319355.1_ASM1531935v1_genomic.fna.gz | prodigal -d GCF_015319355.1_ASM1531935v1_genomic.fna/cds.fna -a GCF_015319355.1_ASM1531935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:30,191] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:30,192] [INFO] Task started: HMMsearch
[2024-01-24 12:06:30,192] [INFO] Running command: hmmsearch --tblout GCF_015319355.1_ASM1531935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/reference_markers.hmm GCF_015319355.1_ASM1531935v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,557] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,600] [INFO] Query marker FASTA was written to GCF_015319355.1_ASM1531935v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,601] [INFO] Task started: Blastn
[2024-01-24 12:06:30,601] [INFO] Running command: blastn -query GCF_015319355.1_ASM1531935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/reference_markers.fasta -out GCF_015319355.1_ASM1531935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,320] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,325] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:31,325] [INFO] Target genome list was writen to GCF_015319355.1_ASM1531935v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:31,332] [INFO] Task started: fastANI
[2024-01-24 12:06:31,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccc7d23-debe-4133-8a7c-6bf6e75b29dd/GCF_015319355.1_ASM1531935v1_genomic.fna.gz --refList GCF_015319355.1_ASM1531935v1_genomic.fna/target_genomes.txt --output GCF_015319355.1_ASM1531935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,339] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,356] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:45,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:45,356] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	79.3265	617	1512	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	79.2495	541	1512	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.8724	481	1512	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.6818	492	1512	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	78.6179	528	1512	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.4492	482	1512	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	78.3985	406	1512	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	78.3052	450	1512	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	78.1365	397	1512	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1038	467	1512	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.0944	481	1512	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.0044	406	1512	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.8726	296	1512	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.7235	355	1512	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3522	262	1512	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.1046	299	1512	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0976	242	1512	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.7288	150	1512	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.7163	204	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,358] [INFO] DFAST Taxonomy check result was written to GCF_015319355.1_ASM1531935v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/checkm_data
[2024-01-24 12:06:45,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,425] [INFO] Task started: CheckM
[2024-01-24 12:06:45,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015319355.1_ASM1531935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015319355.1_ASM1531935v1_genomic.fna/checkm_input GCF_015319355.1_ASM1531935v1_genomic.fna/checkm_result
[2024-01-24 12:07:30,722] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:30,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:30,751] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:30,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:30,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015319355.1_ASM1531935v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:30,752] [INFO] Task started: Blastn
[2024-01-24 12:07:30,752] [INFO] Running command: blastn -query GCF_015319355.1_ASM1531935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb40cc56-ce14-4f9b-9fea-0169192abb87/dqc_reference/reference_markers_gtdb.fasta -out GCF_015319355.1_ASM1531935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:31,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:31,799] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:31,799] [INFO] Target genome list was writen to GCF_015319355.1_ASM1531935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:31,807] [INFO] Task started: fastANI
[2024-01-24 12:07:31,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccc7d23-debe-4133-8a7c-6bf6e75b29dd/GCF_015319355.1_ASM1531935v1_genomic.fna.gz --refList GCF_015319355.1_ASM1531935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015319355.1_ASM1531935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:40,228] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:40,242] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:40,242] [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_015319355.1	s__Psychroserpens luteus	100.0	1511	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479815.1	s__Psychroserpens sp905479815	83.5468	744	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	83.0601	937	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	82.5684	882	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCF_000799465.1	s__Psychroserpens sp000799465	80.7849	798	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	80.0134	632	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	79.2432	543	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	78.8834	493	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	78.8662	483	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	78.5255	348	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:40,244] [INFO] GTDB search result was written to GCF_015319355.1_ASM1531935v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:40,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:40,248] [INFO] DFAST_QC result json was written to GCF_015319355.1_ASM1531935v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:40,249] [INFO] DFAST_QC completed!
[2024-01-24 12:07:40,249] [INFO] Total running time: 0h1m26s