[2024-01-24 12:29:52,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference
[2024-01-24 12:29:53,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,977] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,977] [INFO] Running command: gunzip -c /var/lib/cwl/stgada48798-c93e-4472-a347-f8025aa1ac45/GCF_001399455.2_ASM139945v2_genomic.fna.gz | prodigal -d GCF_001399455.2_ASM139945v2_genomic.fna/cds.fna -a GCF_001399455.2_ASM139945v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:05,165] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:05,166] [INFO] Task started: HMMsearch
[2024-01-24 12:30:05,166] [INFO] Running command: hmmsearch --tblout GCF_001399455.2_ASM139945v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/reference_markers.hmm GCF_001399455.2_ASM139945v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:05,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:05,485] [INFO] Found 6/6 markers.
[2024-01-24 12:30:05,529] [INFO] Query marker FASTA was written to GCF_001399455.2_ASM139945v2_genomic.fna/markers.fasta
[2024-01-24 12:30:05,529] [INFO] Task started: Blastn
[2024-01-24 12:30:05,529] [INFO] Running command: blastn -query GCF_001399455.2_ASM139945v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/reference_markers.fasta -out GCF_001399455.2_ASM139945v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:06,359] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:06,364] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:06,364] [INFO] Target genome list was writen to GCF_001399455.2_ASM139945v2_genomic.fna/target_genomes.txt
[2024-01-24 12:30:06,373] [INFO] Task started: fastANI
[2024-01-24 12:30:06,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgada48798-c93e-4472-a347-f8025aa1ac45/GCF_001399455.2_ASM139945v2_genomic.fna.gz --refList GCF_001399455.2_ASM139945v2_genomic.fna/target_genomes.txt --output GCF_001399455.2_ASM139945v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:19,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:19,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:19,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:19,041] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:19,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:19,041] [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
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	100.0	1591	1599	95	conclusive
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	87.4405	1266	1599	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	87.3931	1196	1599	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	87.0626	1248	1599	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	82.2455	790	1599	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	82.1457	775	1599	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	81.9475	726	1599	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.3978	461	1599	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.1214	420	1599	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.9765	429	1599	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.9593	428	1599	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.8819	438	1599	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.4803	248	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:19,042] [INFO] DFAST Taxonomy check result was written to GCF_001399455.2_ASM139945v2_genomic.fna/tc_result.tsv
[2024-01-24 12:30:19,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:19,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:19,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/checkm_data
[2024-01-24 12:30:19,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:19,091] [INFO] Task started: CheckM
[2024-01-24 12:30:19,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001399455.2_ASM139945v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001399455.2_ASM139945v2_genomic.fna/checkm_input GCF_001399455.2_ASM139945v2_genomic.fna/checkm_result
[2024-01-24 12:30:57,048] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:57,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,076] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:57,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:57,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001399455.2_ASM139945v2_genomic.fna/markers.fasta)
[2024-01-24 12:30:57,077] [INFO] Task started: Blastn
[2024-01-24 12:30:57,077] [INFO] Running command: blastn -query GCF_001399455.2_ASM139945v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg26d7c1f5-b614-4bb8-83be-0b7143fd79a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001399455.2_ASM139945v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:58,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:58,238] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:58,239] [INFO] Target genome list was writen to GCF_001399455.2_ASM139945v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:58,249] [INFO] Task started: fastANI
[2024-01-24 12:30:58,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgada48798-c93e-4472-a347-f8025aa1ac45/GCF_001399455.2_ASM139945v2_genomic.fna.gz --refList GCF_001399455.2_ASM139945v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001399455.2_ASM139945v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:11,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,563] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:11,564] [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_001399455.2	s__Vibrio bivalvicida	100.0	1591	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	conclusive
GCF_000772105.1	s__Vibrio tubiashii	87.4406	1266	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001695575.1	s__Vibrio europaeus	87.0661	1248	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000775715.1	s__Vibrio tubiashii_A	82.4739	803	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	82.2253	792	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004551525.1	s__Vibrio ouci	82.2155	777	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	82.1054	812	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189255.1	s__Vibrio brasiliensis	82.0011	744	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	81.94	727	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	81.4499	636	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_009811315.1	s__Vibrio atypicus	81.2146	685	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000967495.1	s__Vibrio neptunius	81.0782	580	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_000711795.1	s__Vibrio pacinii	81.0569	620	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,566] [INFO] GTDB search result was written to GCF_001399455.2_ASM139945v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:11,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:11,570] [INFO] DFAST_QC result json was written to GCF_001399455.2_ASM139945v2_genomic.fna/dqc_result.json
[2024-01-24 12:31:11,571] [INFO] DFAST_QC completed!
[2024-01-24 12:31:11,571] [INFO] Total running time: 0h1m19s