[2024-01-24 12:36:35,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,359] [INFO] DQC Reference Directory: /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference
[2024-01-24 12:36:36,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,572] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg29d35515-120d-4cbe-ad7d-9c83bb254ca6/GCF_012396675.1_ASM1239667v1_genomic.fna.gz | prodigal -d GCF_012396675.1_ASM1239667v1_genomic.fna/cds.fna -a GCF_012396675.1_ASM1239667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:50,719] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:50,720] [INFO] Task started: HMMsearch
[2024-01-24 12:36:50,720] [INFO] Running command: hmmsearch --tblout GCF_012396675.1_ASM1239667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/reference_markers.hmm GCF_012396675.1_ASM1239667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:51,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:51,088] [INFO] Found 6/6 markers.
[2024-01-24 12:36:51,136] [INFO] Query marker FASTA was written to GCF_012396675.1_ASM1239667v1_genomic.fna/markers.fasta
[2024-01-24 12:36:51,137] [INFO] Task started: Blastn
[2024-01-24 12:36:51,137] [INFO] Running command: blastn -query GCF_012396675.1_ASM1239667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/reference_markers.fasta -out GCF_012396675.1_ASM1239667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:51,978] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:51,983] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:51,983] [INFO] Target genome list was writen to GCF_012396675.1_ASM1239667v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:51,992] [INFO] Task started: fastANI
[2024-01-24 12:36:51,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg29d35515-120d-4cbe-ad7d-9c83bb254ca6/GCF_012396675.1_ASM1239667v1_genomic.fna.gz --refList GCF_012396675.1_ASM1239667v1_genomic.fna/target_genomes.txt --output GCF_012396675.1_ASM1239667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:05,879] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:05,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:05,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:05,896] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:37:05,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:05,897] [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
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	100.0	1628	1631	95	conclusive
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	99.9991	1602	1631	95	conclusive
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	99.9454	1514	1631	95	conclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	94.3243	1321	1631	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	94.3165	1323	1631	95	below_threshold
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	94.3147	1321	1631	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	94.194	1306	1631	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	93.8592	1320	1631	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.824	1319	1631	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.6819	438	1631	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.1414	399	1631	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	76.2659	56	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:05,898] [INFO] DFAST Taxonomy check result was written to GCF_012396675.1_ASM1239667v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:05,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:05,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:05,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/checkm_data
[2024-01-24 12:37:05,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:05,947] [INFO] Task started: CheckM
[2024-01-24 12:37:05,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396675.1_ASM1239667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396675.1_ASM1239667v1_genomic.fna/checkm_input GCF_012396675.1_ASM1239667v1_genomic.fna/checkm_result
[2024-01-24 12:37:50,455] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:50,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:50,480] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:50,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:50,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396675.1_ASM1239667v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:50,481] [INFO] Task started: Blastn
[2024-01-24 12:37:50,481] [INFO] Running command: blastn -query GCF_012396675.1_ASM1239667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77500c6-8a4f-4b21-b0d2-c4a1f0e96f91/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396675.1_ASM1239667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:51,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:51,870] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:51,871] [INFO] Target genome list was writen to GCF_012396675.1_ASM1239667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:51,888] [INFO] Task started: fastANI
[2024-01-24 12:37:51,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg29d35515-120d-4cbe-ad7d-9c83bb254ca6/GCF_012396675.1_ASM1239667v1_genomic.fna.gz --refList GCF_012396675.1_ASM1239667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396675.1_ASM1239667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:00,715] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:00,725] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:00,725] [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_009183365.2	s__Shewanella algae	99.9991	1602	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	conclusive
GCF_002836945.1	s__Shewanella chilikensis	94.3291	1295	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_002836975.1	s__Shewanella indica	94.1913	1306	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_002777975.1	s__Shewanella carassii	93.8259	1319	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017354985.1	s__Shewanella sp017354985	79.0061	475	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_000015245.1	s__Shewanella amazonensis	78.6957	423	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911865.1	s__Shewanella sp012911865	78.5077	417	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	78.4288	328	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:00,727] [INFO] GTDB search result was written to GCF_012396675.1_ASM1239667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:00,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:00,730] [INFO] DFAST_QC result json was written to GCF_012396675.1_ASM1239667v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:00,731] [INFO] DFAST_QC completed!
[2024-01-24 12:38:00,731] [INFO] Total running time: 0h1m25s