[2024-01-24 12:14:09,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference
[2024-01-24 12:14:11,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,141] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg4878dab5-5450-4e28-94fd-22caf4cb3f7d/GCF_004310325.1_ASM431032v1_genomic.fna.gz | prodigal -d GCF_004310325.1_ASM431032v1_genomic.fna/cds.fna -a GCF_004310325.1_ASM431032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:24,860] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:24,861] [INFO] Task started: HMMsearch
[2024-01-24 12:14:24,861] [INFO] Running command: hmmsearch --tblout GCF_004310325.1_ASM431032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/reference_markers.hmm GCF_004310325.1_ASM431032v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:25,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:25,200] [INFO] Found 6/6 markers.
[2024-01-24 12:14:25,237] [INFO] Query marker FASTA was written to GCF_004310325.1_ASM431032v1_genomic.fna/markers.fasta
[2024-01-24 12:14:25,238] [INFO] Task started: Blastn
[2024-01-24 12:14:25,238] [INFO] Running command: blastn -query GCF_004310325.1_ASM431032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/reference_markers.fasta -out GCF_004310325.1_ASM431032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:25,939] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:25,943] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:25,943] [INFO] Target genome list was writen to GCF_004310325.1_ASM431032v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:25,948] [INFO] Task started: fastANI
[2024-01-24 12:14:25,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg4878dab5-5450-4e28-94fd-22caf4cb3f7d/GCF_004310325.1_ASM431032v1_genomic.fna.gz --refList GCF_004310325.1_ASM431032v1_genomic.fna/target_genomes.txt --output GCF_004310325.1_ASM431032v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:35,901] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:35,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:35,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:35,914] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:35,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:35,915] [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
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	100.0	1245	1250	95	conclusive
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	80.6476	766	1250	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	80.6214	763	1250	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	80.1605	687	1250	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	78.711	425	1250	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.6393	395	1250	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.036	363	1250	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.5712	294	1250	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.4982	309	1250	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.4935	234	1250	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.4292	228	1250	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.3583	299	1250	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.7721	210	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:35,917] [INFO] DFAST Taxonomy check result was written to GCF_004310325.1_ASM431032v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:35,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:35,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:35,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/checkm_data
[2024-01-24 12:14:35,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:35,961] [INFO] Task started: CheckM
[2024-01-24 12:14:35,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310325.1_ASM431032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310325.1_ASM431032v1_genomic.fna/checkm_input GCF_004310325.1_ASM431032v1_genomic.fna/checkm_result
[2024-01-24 12:15:19,394] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:19,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,421] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:19,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:19,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310325.1_ASM431032v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:19,422] [INFO] Task started: Blastn
[2024-01-24 12:15:19,422] [INFO] Running command: blastn -query GCF_004310325.1_ASM431032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9630cf6-0162-4663-807e-be76c3de542b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310325.1_ASM431032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:20,479] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:20,484] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:20,485] [INFO] Target genome list was writen to GCF_004310325.1_ASM431032v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:20,506] [INFO] Task started: fastANI
[2024-01-24 12:15:20,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg4878dab5-5450-4e28-94fd-22caf4cb3f7d/GCF_004310325.1_ASM431032v1_genomic.fna.gz --refList GCF_004310325.1_ASM431032v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310325.1_ASM431032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:28,276] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,284] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:28,285] [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_004310325.1	s__Jejuia sp004310325	100.0	1245	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004310335.1	s__Jejuia pacifica	80.6108	764	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016827605.1	s__Jejuia sp016827605	80.1603	687	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	79.8634	652	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	79.7292	628	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCA_002428965.1	s__Jejuia sp002428965	78.8931	507	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.6885	466	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.6342	295	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.5712	294	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,286] [INFO] GTDB search result was written to GCF_004310325.1_ASM431032v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:28,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:28,291] [INFO] DFAST_QC result json was written to GCF_004310325.1_ASM431032v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:28,291] [INFO] DFAST_QC completed!
[2024-01-24 12:15:28,291] [INFO] Total running time: 0h1m19s