[2024-01-24 13:50:10,338] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference
[2024-01-24 13:50:11,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,779] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba26c16-4f81-46d4-a6f1-23db51555b6e/GCF_003024155.1_ASM302415v1_genomic.fna.gz | prodigal -d GCF_003024155.1_ASM302415v1_genomic.fna/cds.fna -a GCF_003024155.1_ASM302415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:30,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:30,216] [INFO] Task started: HMMsearch
[2024-01-24 13:50:30,216] [INFO] Running command: hmmsearch --tblout GCF_003024155.1_ASM302415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/reference_markers.hmm GCF_003024155.1_ASM302415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:30,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:30,492] [INFO] Found 6/6 markers.
[2024-01-24 13:50:30,534] [INFO] Query marker FASTA was written to GCF_003024155.1_ASM302415v1_genomic.fna/markers.fasta
[2024-01-24 13:50:30,534] [INFO] Task started: Blastn
[2024-01-24 13:50:30,534] [INFO] Running command: blastn -query GCF_003024155.1_ASM302415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/reference_markers.fasta -out GCF_003024155.1_ASM302415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,214] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:31,214] [INFO] Target genome list was writen to GCF_003024155.1_ASM302415v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:31,223] [INFO] Task started: fastANI
[2024-01-24 13:50:31,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba26c16-4f81-46d4-a6f1-23db51555b6e/GCF_003024155.1_ASM302415v1_genomic.fna.gz --refList GCF_003024155.1_ASM302415v1_genomic.fna/target_genomes.txt --output GCF_003024155.1_ASM302415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:44,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:44,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:44,384] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:44,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:44,384] [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
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	100.0	1458	1460	95	conclusive
Gramella flava	strain=JLT2011	GCA_001951155.1	1486245	1486245	type	True	78.7219	391	1460	95	below_threshold
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	78.5376	384	1460	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.3381	386	1460	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	78.3324	273	1460	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.2814	377	1460	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	78.1566	356	1460	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.0813	366	1460	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	78.0415	326	1460	95	below_threshold
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	77.7933	256	1460	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.3344	222	1460	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	77.2755	226	1460	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.1662	171	1460	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.85	59	1460	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.6772	55	1460	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	75.9225	52	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:44,386] [INFO] DFAST Taxonomy check result was written to GCF_003024155.1_ASM302415v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:44,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:44,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:44,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/checkm_data
[2024-01-24 13:50:44,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:44,428] [INFO] Task started: CheckM
[2024-01-24 13:50:44,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024155.1_ASM302415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024155.1_ASM302415v1_genomic.fna/checkm_input GCF_003024155.1_ASM302415v1_genomic.fna/checkm_result
[2024-01-24 13:51:35,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:35,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:35,471] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:35,472] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:35,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024155.1_ASM302415v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:35,472] [INFO] Task started: Blastn
[2024-01-24 13:51:35,473] [INFO] Running command: blastn -query GCF_003024155.1_ASM302415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff427a27-77eb-43f7-b326-8b5322a1977d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024155.1_ASM302415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:36,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:36,306] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:36,306] [INFO] Target genome list was writen to GCF_003024155.1_ASM302415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:36,358] [INFO] Task started: fastANI
[2024-01-24 13:51:36,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba26c16-4f81-46d4-a6f1-23db51555b6e/GCF_003024155.1_ASM302415v1_genomic.fna.gz --refList GCF_003024155.1_ASM302415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024155.1_ASM302415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:48,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:48,553] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:48,553] [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_003024155.1	s__Gramella fulva	100.0	1458	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009735695.1	s__Gramella sp009735695	78.7688	372	1460	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	78.7202	393	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	-
GCF_000423065.1	s__Gramella echinicola	78.4702	322	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_001889005.1	s__Gramella salexigens	78.3797	275	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.2961	375	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004332155.1	s__Gramella sp004332155	78.2808	331	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	78.1609	355	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105135.1	s__Gramella sp900105135	78.1474	346	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	78.1277	300	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	78.0396	323	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423045.1	s__Gramella portivictoriae	77.7838	256	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078605.1	s__Salegentibacter sediminis	77.3207	191	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	77.2967	225	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_014651535.1	s__Salinimicrobium marinum	77.0975	170	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:48,555] [INFO] GTDB search result was written to GCF_003024155.1_ASM302415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:48,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:48,559] [INFO] DFAST_QC result json was written to GCF_003024155.1_ASM302415v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:48,559] [INFO] DFAST_QC completed!
[2024-01-24 13:51:48,559] [INFO] Total running time: 0h1m38s