[2024-01-24 15:18:27,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference
[2024-01-24 15:18:28,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,903] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f26a271-a311-4d36-ab20-409a2cbb2fc6/GCF_007989585.1_ASM798958v1_genomic.fna.gz | prodigal -d GCF_007989585.1_ASM798958v1_genomic.fna/cds.fna -a GCF_007989585.1_ASM798958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:37,541] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:37,541] [INFO] Task started: HMMsearch
[2024-01-24 15:18:37,541] [INFO] Running command: hmmsearch --tblout GCF_007989585.1_ASM798958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/reference_markers.hmm GCF_007989585.1_ASM798958v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:37,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:37,926] [INFO] Found 6/6 markers.
[2024-01-24 15:18:37,994] [INFO] Query marker FASTA was written to GCF_007989585.1_ASM798958v1_genomic.fna/markers.fasta
[2024-01-24 15:18:37,994] [INFO] Task started: Blastn
[2024-01-24 15:18:37,995] [INFO] Running command: blastn -query GCF_007989585.1_ASM798958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/reference_markers.fasta -out GCF_007989585.1_ASM798958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:38,855] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:38,863] [INFO] Selected 10 target genomes.
[2024-01-24 15:18:38,863] [INFO] Target genome list was writen to GCF_007989585.1_ASM798958v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:38,869] [INFO] Task started: fastANI
[2024-01-24 15:18:38,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f26a271-a311-4d36-ab20-409a2cbb2fc6/GCF_007989585.1_ASM798958v1_genomic.fna.gz --refList GCF_007989585.1_ASM798958v1_genomic.fna/target_genomes.txt --output GCF_007989585.1_ASM798958v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:48,808] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:48,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:48,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:48,818] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:48,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:48,818] [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 espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	100.0	1413	1417	95	conclusive
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	99.9988	1416	1417	95	conclusive
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	88.0634	1057	1417	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	87.9782	1090	1417	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	87.8451	1115	1417	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	83.5672	1026	1417	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.112	590	1417	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.5924	52	1417	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.4639	58	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:48,821] [INFO] DFAST Taxonomy check result was written to GCF_007989585.1_ASM798958v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:48,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:48,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:48,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/checkm_data
[2024-01-24 15:18:48,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:48,866] [INFO] Task started: CheckM
[2024-01-24 15:18:48,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989585.1_ASM798958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989585.1_ASM798958v1_genomic.fna/checkm_input GCF_007989585.1_ASM798958v1_genomic.fna/checkm_result
[2024-01-24 15:19:19,055] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:19,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:19,079] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:19,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:19,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989585.1_ASM798958v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:19,080] [INFO] Task started: Blastn
[2024-01-24 15:19:19,081] [INFO] Running command: blastn -query GCF_007989585.1_ASM798958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cfef39a-d5b8-44d2-a83c-e500db5a21c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989585.1_ASM798958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:20,246] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:20,250] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:20,250] [INFO] Target genome list was writen to GCF_007989585.1_ASM798958v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:20,258] [INFO] Task started: fastANI
[2024-01-24 15:19:20,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f26a271-a311-4d36-ab20-409a2cbb2fc6/GCF_007989585.1_ASM798958v1_genomic.fna.gz --refList GCF_007989585.1_ASM798958v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989585.1_ASM798958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:28,902] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:28,916] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:28,917] [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_002221525.1	s__Pseudoalteromonas espejiana	99.9988	1416	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	87.8355	1116	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	87.4327	1114	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_001401805.1	s__Pseudoalteromonas sp001401805	87.4124	1115	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.16	97.37	0.91	0.90	5	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	86.7221	1031	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_001468485.1	s__Pseudoalteromonas sp001468485	83.7279	876	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	83.3244	967	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238275.3	s__Pseudoalteromonas undina	81.5378	727	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,919] [INFO] GTDB search result was written to GCF_007989585.1_ASM798958v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:28,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:28,924] [INFO] DFAST_QC result json was written to GCF_007989585.1_ASM798958v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:28,924] [INFO] DFAST_QC completed!
[2024-01-24 15:19:28,924] [INFO] Total running time: 0h1m1s