[2024-01-25 17:51:20,517] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:20,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:20,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference
[2024-01-25 17:51:21,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:21,732] [INFO] Task started: Prodigal
[2024-01-25 17:51:21,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgd84e3da3-818c-4d2c-b135-d1de300205e7/GCF_001541335.1_ASM154133v1_genomic.fna.gz | prodigal -d GCF_001541335.1_ASM154133v1_genomic.fna/cds.fna -a GCF_001541335.1_ASM154133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:30,821] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:30,821] [INFO] Task started: HMMsearch
[2024-01-25 17:51:30,821] [INFO] Running command: hmmsearch --tblout GCF_001541335.1_ASM154133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/reference_markers.hmm GCF_001541335.1_ASM154133v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:31,043] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:31,044] [INFO] Found 6/6 markers.
[2024-01-25 17:51:31,106] [INFO] Query marker FASTA was written to GCF_001541335.1_ASM154133v1_genomic.fna/markers.fasta
[2024-01-25 17:51:31,107] [INFO] Task started: Blastn
[2024-01-25 17:51:31,107] [INFO] Running command: blastn -query GCF_001541335.1_ASM154133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/reference_markers.fasta -out GCF_001541335.1_ASM154133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:31,842] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:31,845] [INFO] Selected 11 target genomes.
[2024-01-25 17:51:31,845] [INFO] Target genome list was writen to GCF_001541335.1_ASM154133v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:31,860] [INFO] Task started: fastANI
[2024-01-25 17:51:31,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84e3da3-818c-4d2c-b135-d1de300205e7/GCF_001541335.1_ASM154133v1_genomic.fna.gz --refList GCF_001541335.1_ASM154133v1_genomic.fna/target_genomes.txt --output GCF_001541335.1_ASM154133v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:44,731] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:44,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:44,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:44,739] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:51:44,739] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:51:44,739] [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 toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	100.0	1466	1467	95	inconclusive
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	99.9983	1465	1467	95	inconclusive
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	99.9982	1465	1467	95	inconclusive
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	95.4267	1321	1467	95	inconclusive
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	95.3656	1339	1467	95	inconclusive
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	89.5504	1259	1467	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	88.3185	1234	1467	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	88.2126	1220	1467	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	88.021	1205	1467	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	87.9494	1232	1467	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	87.8564	1226	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:44,741] [INFO] DFAST Taxonomy check result was written to GCF_001541335.1_ASM154133v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:44,741] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:44,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:44,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/checkm_data
[2024-01-25 17:51:44,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:44,787] [INFO] Task started: CheckM
[2024-01-25 17:51:44,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001541335.1_ASM154133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001541335.1_ASM154133v1_genomic.fna/checkm_input GCF_001541335.1_ASM154133v1_genomic.fna/checkm_result
[2024-01-25 17:52:15,737] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:15,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:15,762] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:15,762] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:15,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001541335.1_ASM154133v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:15,764] [INFO] Task started: Blastn
[2024-01-25 17:52:15,764] [INFO] Running command: blastn -query GCF_001541335.1_ASM154133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8717a401-916a-4a68-8361-42b950508a42/dqc_reference/reference_markers_gtdb.fasta -out GCF_001541335.1_ASM154133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:16,899] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:16,902] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:16,902] [INFO] Target genome list was writen to GCF_001541335.1_ASM154133v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:16,910] [INFO] Task started: fastANI
[2024-01-25 17:52:16,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84e3da3-818c-4d2c-b135-d1de300205e7/GCF_001541335.1_ASM154133v1_genomic.fna.gz --refList GCF_001541335.1_ASM154133v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001541335.1_ASM154133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:34,667] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:34,676] [INFO] Found 15 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 17:52:34,677] [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_900089765.1	s__Vibrio toranzoniae	99.9982	1465	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	inconclusive
GCF_008801285.1	s__Vibrio kanaloae	95.4267	1321	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	inconclusive
GCF_013394185.1	s__Vibrio sp013394185	89.5457	1234	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	89.3704	1135	1467	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	88.7256	1220	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_000272105.2	s__Vibrio splendidus_I	88.4794	1190	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156455.1	s__Vibrio coralliirubri	88.4476	1157	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_002875945.1	s__Vibrio lentus_A	88.3474	1203	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858795.1	s__Vibrio sp007858795	88.3219	1214	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156525.1	s__Vibrio celticus	88.3124	1197	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_014878155.1	s__Vibrio lentus	88.1411	1194	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_002156475.1	s__Vibrio gigantis	88.0131	1206	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_002875705.1	s__Vibrio sp002875705	87.9043	1161	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_014879975.1	s__Vibrio bathopelagicus	87.8652	1225	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	87.5663	1114	1467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:34,678] [INFO] GTDB search result was written to GCF_001541335.1_ASM154133v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:34,679] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:34,684] [INFO] DFAST_QC result json was written to GCF_001541335.1_ASM154133v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:34,684] [INFO] DFAST_QC completed!
[2024-01-25 17:52:34,684] [INFO] Total running time: 0h1m14s