[2024-01-24 13:18:40,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:40,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:40,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference
[2024-01-24 13:18:41,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:41,910] [INFO] Task started: Prodigal
[2024-01-24 13:18:41,910] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0f4f15c-bd81-41ac-bc17-f75f88df7969/GCF_014858715.1_ASM1485871v1_genomic.fna.gz | prodigal -d GCF_014858715.1_ASM1485871v1_genomic.fna/cds.fna -a GCF_014858715.1_ASM1485871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:54,565] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:54,565] [INFO] Task started: HMMsearch
[2024-01-24 13:18:54,565] [INFO] Running command: hmmsearch --tblout GCF_014858715.1_ASM1485871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/reference_markers.hmm GCF_014858715.1_ASM1485871v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:54,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:54,913] [INFO] Found 6/6 markers.
[2024-01-24 13:18:54,966] [INFO] Query marker FASTA was written to GCF_014858715.1_ASM1485871v1_genomic.fna/markers.fasta
[2024-01-24 13:18:54,967] [INFO] Task started: Blastn
[2024-01-24 13:18:54,967] [INFO] Running command: blastn -query GCF_014858715.1_ASM1485871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/reference_markers.fasta -out GCF_014858715.1_ASM1485871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:55,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:55,846] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:55,846] [INFO] Target genome list was writen to GCF_014858715.1_ASM1485871v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:55,853] [INFO] Task started: fastANI
[2024-01-24 13:18:55,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f4f15c-bd81-41ac-bc17-f75f88df7969/GCF_014858715.1_ASM1485871v1_genomic.fna.gz --refList GCF_014858715.1_ASM1485871v1_genomic.fna/target_genomes.txt --output GCF_014858715.1_ASM1485871v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:06,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:06,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:06,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:06,810] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:19:06,811] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:06,811] [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 flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	100.0	1810	1810	95	inconclusive
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	99.9758	1760	1810	95	inconclusive
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	96.1366	1545	1810	95	inconclusive
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	96.08	1581	1810	95	inconclusive
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	92.7657	1443	1810	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.196	208	1810	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	77.7892	235	1810	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.3357	59	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,812] [INFO] DFAST Taxonomy check result was written to GCF_014858715.1_ASM1485871v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:06,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:06,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:06,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/checkm_data
[2024-01-24 13:19:06,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:06,862] [INFO] Task started: CheckM
[2024-01-24 13:19:06,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014858715.1_ASM1485871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014858715.1_ASM1485871v1_genomic.fna/checkm_input GCF_014858715.1_ASM1485871v1_genomic.fna/checkm_result
[2024-01-24 13:19:49,013] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:49,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,033] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:49,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:49,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014858715.1_ASM1485871v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:49,034] [INFO] Task started: Blastn
[2024-01-24 13:19:49,034] [INFO] Running command: blastn -query GCF_014858715.1_ASM1485871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7899278a-4ff2-4dfc-bf14-a95b1a7d17ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_014858715.1_ASM1485871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:50,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:50,253] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:50,253] [INFO] Target genome list was writen to GCF_014858715.1_ASM1485871v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:50,259] [INFO] Task started: fastANI
[2024-01-24 13:19:50,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f4f15c-bd81-41ac-bc17-f75f88df7969/GCF_014858715.1_ASM1485871v1_genomic.fna.gz --refList GCF_014858715.1_ASM1485871v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014858715.1_ASM1485871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:02,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:02,385] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:02,385] [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
GCA_000814665.1	s__Pseudoalteromonas elyakovii	99.9645	1784	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	98.47	97.40	0.94	0.89	9	conclusive
GCF_000238315.3	s__Pseudoalteromonas piscicida	96.08	1581	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	-
GCF_016695175.1	s__Pseudoalteromonas sp002591815	95.5466	1590	1810	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	95.3944	1523	1810	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	94.9993	1466	1810	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	94.3661	1417	1810	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	93.5004	1517	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:02,386] [INFO] GTDB search result was written to GCF_014858715.1_ASM1485871v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:02,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:02,389] [INFO] DFAST_QC result json was written to GCF_014858715.1_ASM1485871v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:02,390] [INFO] DFAST_QC completed!
[2024-01-24 13:20:02,390] [INFO] Total running time: 0h1m22s