[2024-01-24 13:57:27,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:27,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:27,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference
[2024-01-24 13:57:28,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:28,710] [INFO] Task started: Prodigal
[2024-01-24 13:57:28,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c0c899b-7d64-4e53-bd09-8ebb5ac2f638/GCF_002156475.1_ASM215647v1_genomic.fna.gz | prodigal -d GCF_002156475.1_ASM215647v1_genomic.fna/cds.fna -a GCF_002156475.1_ASM215647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:42,524] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:42,524] [INFO] Task started: HMMsearch
[2024-01-24 13:57:42,524] [INFO] Running command: hmmsearch --tblout GCF_002156475.1_ASM215647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/reference_markers.hmm GCF_002156475.1_ASM215647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:42,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:42,970] [INFO] Found 6/6 markers.
[2024-01-24 13:57:43,033] [INFO] Query marker FASTA was written to GCF_002156475.1_ASM215647v1_genomic.fna/markers.fasta
[2024-01-24 13:57:43,033] [INFO] Task started: Blastn
[2024-01-24 13:57:43,033] [INFO] Running command: blastn -query GCF_002156475.1_ASM215647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/reference_markers.fasta -out GCF_002156475.1_ASM215647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:43,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:43,813] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:43,813] [INFO] Target genome list was writen to GCF_002156475.1_ASM215647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:43,818] [INFO] Task started: fastANI
[2024-01-24 13:57:43,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0c899b-7d64-4e53-bd09-8ebb5ac2f638/GCF_002156475.1_ASM215647v1_genomic.fna.gz --refList GCF_002156475.1_ASM215647v1_genomic.fna/target_genomes.txt --output GCF_002156475.1_ASM215647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:03,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:03,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:03,726] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:03,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:03,726] [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 gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	100.0	1854	1855	95	conclusive
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	99.9966	1854	1855	95	conclusive
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	90.853	1395	1855	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	90.8347	1435	1855	95	below_threshold
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	90.7637	1297	1855	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	90.6806	1353	1855	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	90.6534	1314	1855	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	90.5412	1435	1855	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	90.4856	1352	1855	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	90.2872	1442	1855	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	90.2724	1491	1855	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	88.4718	1262	1855	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	88.41	1287	1855	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	87.8032	1308	1855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,728] [INFO] DFAST Taxonomy check result was written to GCF_002156475.1_ASM215647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:03,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:03,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:03,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/checkm_data
[2024-01-24 13:58:03,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:03,783] [INFO] Task started: CheckM
[2024-01-24 13:58:03,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156475.1_ASM215647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156475.1_ASM215647v1_genomic.fna/checkm_input GCF_002156475.1_ASM215647v1_genomic.fna/checkm_result
[2024-01-24 13:58:48,935] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:48,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:48,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:48,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156475.1_ASM215647v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:48,971] [INFO] Task started: Blastn
[2024-01-24 13:58:48,971] [INFO] Running command: blastn -query GCF_002156475.1_ASM215647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg348d99de-956e-41b7-89eb-14c12b3bccb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156475.1_ASM215647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,927] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,930] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:49,930] [INFO] Target genome list was writen to GCF_002156475.1_ASM215647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,933] [INFO] Task started: fastANI
[2024-01-24 13:58:49,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0c899b-7d64-4e53-bd09-8ebb5ac2f638/GCF_002156475.1_ASM215647v1_genomic.fna.gz --refList GCF_002156475.1_ASM215647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156475.1_ASM215647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,038] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,038] [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_002156475.1	s__Vibrio gigantis	100.0	1854	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	conclusive
GCF_007858795.1	s__Vibrio sp007858795	91.6844	1437	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048535.1	s__Vibrio crassostreae	90.8555	1394	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_001557875.1	s__Vibrio splendidus_F	90.7922	1440	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_002156525.1	s__Vibrio celticus	90.7637	1297	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_002156455.1	s__Vibrio coralliirubri	90.6806	1353	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_000272045.2	s__Vibrio crassostreae_C	90.6204	1332	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272105.2	s__Vibrio splendidus_I	90.5301	1298	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394185.1	s__Vibrio sp013394185	90.4309	1405	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014879975.1	s__Vibrio bathopelagicus	90.2724	1491	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316985.1	s__Vibrio sp000316985	90.2402	1301	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	90.0668	1361	1855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,040] [INFO] GTDB search result was written to GCF_002156475.1_ASM215647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,043] [INFO] DFAST_QC result json was written to GCF_002156475.1_ASM215647v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,043] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,043] [INFO] Total running time: 0h1m38s