[2024-01-24 11:12:39,762] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference
[2024-01-24 11:12:41,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,106] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,107] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe196f71-c848-499f-89e4-856b36042eca/GCF_014925405.1_ASM1492540v1_genomic.fna.gz | prodigal -d GCF_014925405.1_ASM1492540v1_genomic.fna/cds.fna -a GCF_014925405.1_ASM1492540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:51,803] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:51,804] [INFO] Task started: HMMsearch
[2024-01-24 11:12:51,804] [INFO] Running command: hmmsearch --tblout GCF_014925405.1_ASM1492540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/reference_markers.hmm GCF_014925405.1_ASM1492540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:52,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:52,128] [INFO] Found 6/6 markers.
[2024-01-24 11:12:52,173] [INFO] Query marker FASTA was written to GCF_014925405.1_ASM1492540v1_genomic.fna/markers.fasta
[2024-01-24 11:12:52,173] [INFO] Task started: Blastn
[2024-01-24 11:12:52,173] [INFO] Running command: blastn -query GCF_014925405.1_ASM1492540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/reference_markers.fasta -out GCF_014925405.1_ASM1492540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:52,911] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:52,917] [INFO] Selected 19 target genomes.
[2024-01-24 11:12:52,918] [INFO] Target genome list was writen to GCF_014925405.1_ASM1492540v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:52,936] [INFO] Task started: fastANI
[2024-01-24 11:12:52,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe196f71-c848-499f-89e4-856b36042eca/GCF_014925405.1_ASM1492540v1_genomic.fna.gz --refList GCF_014925405.1_ASM1492540v1_genomic.fna/target_genomes.txt --output GCF_014925405.1_ASM1492540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,536] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,556] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:08,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,556] [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
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	100.0	1565	1566	95	conclusive
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	79.9102	619	1566	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_003568825.1	314281	314281	type	True	79.91	613	1566	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	79.8667	618	1566	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	78.6831	214	1566	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	78.6725	230	1566	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	78.5481	208	1566	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	78.5435	227	1566	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	78.3074	219	1566	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	78.2837	202	1566	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	78.2059	191	1566	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	78.2053	199	1566	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	78.1562	197	1566	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	78.0857	209	1566	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.8967	70	1566	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	76.6631	50	1566	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.5748	70	1566	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	76.4974	53	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,558] [INFO] DFAST Taxonomy check result was written to GCF_014925405.1_ASM1492540v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/checkm_data
[2024-01-24 11:13:08,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,607] [INFO] Task started: CheckM
[2024-01-24 11:13:08,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925405.1_ASM1492540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925405.1_ASM1492540v1_genomic.fna/checkm_input GCF_014925405.1_ASM1492540v1_genomic.fna/checkm_result
[2024-01-24 11:13:44,690] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:44,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:44,715] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:44,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:44,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925405.1_ASM1492540v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:44,716] [INFO] Task started: Blastn
[2024-01-24 11:13:44,717] [INFO] Running command: blastn -query GCF_014925405.1_ASM1492540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg631f1e8a-7923-47e7-9c25-e9e351d30609/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925405.1_ASM1492540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:45,914] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:45,917] [INFO] Selected 21 target genomes.
[2024-01-24 11:13:45,918] [INFO] Target genome list was writen to GCF_014925405.1_ASM1492540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:45,936] [INFO] Task started: fastANI
[2024-01-24 11:13:45,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe196f71-c848-499f-89e4-856b36042eca/GCF_014925405.1_ASM1492540v1_genomic.fna.gz --refList GCF_014925405.1_ASM1492540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925405.1_ASM1492540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:02,349] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:02,369] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:02,369] [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_014925405.1	s__Pseudoalteromonas ulvae	100.0	1565	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.81	98.81	0.93	0.93	2	conclusive
GCF_002310815.1	s__Pseudoalteromonas tunicata	79.9117	619	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	78.8187	233	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	78.6637	229	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	78.6126	192	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	78.6034	214	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_000238275.3	s__Pseudoalteromonas undina	78.5579	228	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	78.5481	208	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	78.4434	232	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	78.4111	234	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	78.4078	243	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000788395.1	s__Pseudoalteromonas piratica	78.2837	202	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	78.2801	220	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	78.2409	236	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238375.3	s__Pseudoalteromonas citrea	78.0705	210	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	78.0339	234	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	77.9626	202	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269985.1	s__Pseudoalteromonas sp001269985	77.9326	230	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.50	95.03	0.90	0.80	3	-
GCF_014905615.1	s__Pseudoalteromonas aliena	77.8985	223	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
GCF_001401805.1	s__Pseudoalteromonas sp001401805	77.8574	210	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.16	97.37	0.91	0.90	5	-
GCF_001399975.1	s__Pseudoalteromonas sp001399975	77.8222	218	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:02,371] [INFO] GTDB search result was written to GCF_014925405.1_ASM1492540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:02,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:02,376] [INFO] DFAST_QC result json was written to GCF_014925405.1_ASM1492540v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:02,376] [INFO] DFAST_QC completed!
[2024-01-24 11:14:02,376] [INFO] Total running time: 0h1m23s