[2023-06-27 00:46:11,100] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:46:11,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:46:11,121] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference
[2023-06-27 00:46:12,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:46:12,302] [INFO] Task started: Prodigal
[2023-06-27 00:46:12,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg7df373a2-4b3d-4115-9550-f473af39ad81/GCA_002435155.1_ASM243515v1_genomic.fna.gz | prodigal -d GCA_002435155.1_ASM243515v1_genomic.fna/cds.fna -a GCA_002435155.1_ASM243515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:46:19,041] [INFO] Task succeeded: Prodigal
[2023-06-27 00:46:19,042] [INFO] Task started: HMMsearch
[2023-06-27 00:46:19,042] [INFO] Running command: hmmsearch --tblout GCA_002435155.1_ASM243515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/reference_markers.hmm GCA_002435155.1_ASM243515v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:46:19,318] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:46:19,320] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7df373a2-4b3d-4115-9550-f473af39ad81/GCA_002435155.1_ASM243515v1_genomic.fna.gz]
[2023-06-27 00:46:19,356] [INFO] Query marker FASTA was written to GCA_002435155.1_ASM243515v1_genomic.fna/markers.fasta
[2023-06-27 00:46:19,357] [INFO] Task started: Blastn
[2023-06-27 00:46:19,357] [INFO] Running command: blastn -query GCA_002435155.1_ASM243515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/reference_markers.fasta -out GCA_002435155.1_ASM243515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:46:19,990] [INFO] Task succeeded: Blastn
[2023-06-27 00:46:19,996] [INFO] Selected 11 target genomes.
[2023-06-27 00:46:19,996] [INFO] Target genome list was writen to GCA_002435155.1_ASM243515v1_genomic.fna/target_genomes.txt
[2023-06-27 00:46:19,999] [INFO] Task started: fastANI
[2023-06-27 00:46:19,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg7df373a2-4b3d-4115-9550-f473af39ad81/GCA_002435155.1_ASM243515v1_genomic.fna.gz --refList GCA_002435155.1_ASM243515v1_genomic.fna/target_genomes.txt --output GCA_002435155.1_ASM243515v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:46:29,693] [INFO] Task succeeded: fastANI
[2023-06-27 00:46:29,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:46:29,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:46:29,707] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 00:46:29,707] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 00:46:29,708] [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=ATCC 29659	GCA_002221525.1	28107	28107	type	True	87.1382	1018	1206	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	87.0826	1001	1206	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	85.8597	933	1206	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	85.8278	904	1206	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	85.7932	945	1206	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.8357	822	1206	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	82.4159	801	1206	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	79.5423	502	1206	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	75.9741	54	1206	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.7097	51	1206	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:46:29,710] [INFO] DFAST Taxonomy check result was written to GCA_002435155.1_ASM243515v1_genomic.fna/tc_result.tsv
[2023-06-27 00:46:29,710] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:46:29,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:46:29,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/checkm_data
[2023-06-27 00:46:29,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:46:29,759] [INFO] Task started: CheckM
[2023-06-27 00:46:29,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002435155.1_ASM243515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002435155.1_ASM243515v1_genomic.fna/checkm_input GCA_002435155.1_ASM243515v1_genomic.fna/checkm_result
[2023-06-27 00:46:55,080] [INFO] Task succeeded: CheckM
[2023-06-27 00:46:55,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 00:46:55,104] [INFO] ===== Completeness check finished =====
[2023-06-27 00:46:55,105] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:46:55,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002435155.1_ASM243515v1_genomic.fna/markers.fasta)
[2023-06-27 00:46:55,105] [INFO] Task started: Blastn
[2023-06-27 00:46:55,105] [INFO] Running command: blastn -query GCA_002435155.1_ASM243515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8798f5-24af-49e5-85ba-7efbfc9cfdc2/dqc_reference/reference_markers_gtdb.fasta -out GCA_002435155.1_ASM243515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:46:56,048] [INFO] Task succeeded: Blastn
[2023-06-27 00:46:56,052] [INFO] Selected 7 target genomes.
[2023-06-27 00:46:56,052] [INFO] Target genome list was writen to GCA_002435155.1_ASM243515v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:46:56,062] [INFO] Task started: fastANI
[2023-06-27 00:46:56,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg7df373a2-4b3d-4115-9550-f473af39ad81/GCA_002435155.1_ASM243515v1_genomic.fna.gz --refList GCA_002435155.1_ASM243515v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002435155.1_ASM243515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:47:03,106] [INFO] Task succeeded: fastANI
[2023-06-27 00:47:03,118] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 00:47:03,119] [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_007988745.1	s__Pseudoalteromonas atlantica	97.9351	1092	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	conclusive
GCF_001401805.1	s__Pseudoalteromonas sp001401805	92.3549	1046	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.16	97.37	0.91	0.90	5	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	87.142	1018	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	85.794	945	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	84.7905	857	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	82.5322	786	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238395.3	s__Pseudoalteromonas arctica	82.4251	800	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
--------------------------------------------------------------------------------
[2023-06-27 00:47:03,121] [INFO] GTDB search result was written to GCA_002435155.1_ASM243515v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:47:03,122] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:47:03,125] [INFO] DFAST_QC result json was written to GCA_002435155.1_ASM243515v1_genomic.fna/dqc_result.json
[2023-06-27 00:47:03,125] [INFO] DFAST_QC completed!
[2023-06-27 00:47:03,125] [INFO] Total running time: 0h0m52s