[2024-01-25 20:07:05,491] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:05,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:05,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference
[2024-01-25 20:07:06,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:06,628] [INFO] Task started: Prodigal
[2024-01-25 20:07:06,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg76f790c9-ae03-4d29-a79a-d30a471e842f/GCF_000382005.1_ASM38200v1_genomic.fna.gz | prodigal -d GCF_000382005.1_ASM38200v1_genomic.fna/cds.fna -a GCF_000382005.1_ASM38200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:17,013] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:17,013] [INFO] Task started: HMMsearch
[2024-01-25 20:07:17,013] [INFO] Running command: hmmsearch --tblout GCF_000382005.1_ASM38200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/reference_markers.hmm GCF_000382005.1_ASM38200v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:17,288] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:17,289] [INFO] Found 6/6 markers.
[2024-01-25 20:07:17,333] [INFO] Query marker FASTA was written to GCF_000382005.1_ASM38200v1_genomic.fna/markers.fasta
[2024-01-25 20:07:17,334] [INFO] Task started: Blastn
[2024-01-25 20:07:17,334] [INFO] Running command: blastn -query GCF_000382005.1_ASM38200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/reference_markers.fasta -out GCF_000382005.1_ASM38200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:18,037] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:18,040] [INFO] Selected 9 target genomes.
[2024-01-25 20:07:18,040] [INFO] Target genome list was writen to GCF_000382005.1_ASM38200v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:18,045] [INFO] Task started: fastANI
[2024-01-25 20:07:18,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f790c9-ae03-4d29-a79a-d30a471e842f/GCF_000382005.1_ASM38200v1_genomic.fna.gz --refList GCF_000382005.1_ASM38200v1_genomic.fna/target_genomes.txt --output GCF_000382005.1_ASM38200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:29,613] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:29,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:29,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:29,621] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:07:29,621] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:07:29,621] [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 piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	100.0	1724	1729	95	inconclusive
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	99.9695	1729	1729	95	inconclusive
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	96.1499	1540	1729	95	inconclusive
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	96.1388	1534	1729	95	inconclusive
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	92.5068	1402	1729	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	77.8037	245	1729	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	77.743	201	1729	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.1544	50	1729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:29,622] [INFO] DFAST Taxonomy check result was written to GCF_000382005.1_ASM38200v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:29,623] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:29,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:29,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/checkm_data
[2024-01-25 20:07:29,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:29,673] [INFO] Task started: CheckM
[2024-01-25 20:07:29,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382005.1_ASM38200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382005.1_ASM38200v1_genomic.fna/checkm_input GCF_000382005.1_ASM38200v1_genomic.fna/checkm_result
[2024-01-25 20:08:03,439] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:03,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:03,468] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:03,468] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:03,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382005.1_ASM38200v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:03,469] [INFO] Task started: Blastn
[2024-01-25 20:08:03,469] [INFO] Running command: blastn -query GCF_000382005.1_ASM38200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf2f3cc-2d23-48c1-b4a5-6cc5eefdedfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382005.1_ASM38200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:04,604] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:04,607] [INFO] Selected 8 target genomes.
[2024-01-25 20:08:04,607] [INFO] Target genome list was writen to GCF_000382005.1_ASM38200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:04,616] [INFO] Task started: fastANI
[2024-01-25 20:08:04,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f790c9-ae03-4d29-a79a-d30a471e842f/GCF_000382005.1_ASM38200v1_genomic.fna.gz --refList GCF_000382005.1_ASM38200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382005.1_ASM38200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:17,568] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:17,574] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 20:08:17,574] [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_000238315.3	s__Pseudoalteromonas piscicida	99.9695	1729	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	inconclusive
GCA_000814665.1	s__Pseudoalteromonas elyakovii	96.136	1539	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	98.47	97.40	0.94	0.89	9	inconclusive
GCF_016695175.1	s__Pseudoalteromonas sp002591815	95.4043	1558	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6666	100.00	100.00	1.00	1.00	2	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	95.0903	1508	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	94.6388	1438	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_005886535.1	s__Pseudoalteromonas sp005886535	94.2197	1449	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002208135.1	s__Pseudoalteromonas piscicida_A	93.7277	1499	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
GCF_004103285.1	s__Pseudoalteromonas sp004103285	92.53	1371	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:17,576] [INFO] GTDB search result was written to GCF_000382005.1_ASM38200v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:17,576] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:17,579] [INFO] DFAST_QC result json was written to GCF_000382005.1_ASM38200v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:17,579] [INFO] DFAST_QC completed!
[2024-01-25 20:08:17,579] [INFO] Total running time: 0h1m12s