[2024-01-24 11:51:50,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference
[2024-01-24 11:51:51,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,547] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg49d0ee21-1235-4d2b-8e35-3764fd3dab36/GCF_003217175.1_ASM321717v1_genomic.fna.gz | prodigal -d GCF_003217175.1_ASM321717v1_genomic.fna/cds.fna -a GCF_003217175.1_ASM321717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:03,906] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:03,906] [INFO] Task started: HMMsearch
[2024-01-24 11:52:03,907] [INFO] Running command: hmmsearch --tblout GCF_003217175.1_ASM321717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/reference_markers.hmm GCF_003217175.1_ASM321717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:04,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:04,172] [INFO] Found 6/6 markers.
[2024-01-24 11:52:04,212] [INFO] Query marker FASTA was written to GCF_003217175.1_ASM321717v1_genomic.fna/markers.fasta
[2024-01-24 11:52:04,213] [INFO] Task started: Blastn
[2024-01-24 11:52:04,213] [INFO] Running command: blastn -query GCF_003217175.1_ASM321717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/reference_markers.fasta -out GCF_003217175.1_ASM321717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:05,044] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:05,047] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:05,048] [INFO] Target genome list was writen to GCF_003217175.1_ASM321717v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:05,052] [INFO] Task started: fastANI
[2024-01-24 11:52:05,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d0ee21-1235-4d2b-8e35-3764fd3dab36/GCF_003217175.1_ASM321717v1_genomic.fna.gz --refList GCF_003217175.1_ASM321717v1_genomic.fna/target_genomes.txt --output GCF_003217175.1_ASM321717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:16,683] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:16,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:16,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:16,696] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:52:16,696] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:52:16,696] [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 chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	100.0	1434	1436	95	inconclusive
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	99.9955	1422	1436	95	inconclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	99.9815	1408	1436	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_002836945.1	558541	558541	type	True	99.9673	1378	1436	95	inconclusive
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	95.7929	1326	1436	95	inconclusive
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	94.4967	1257	1436	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.483	1240	1436	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	78.57	392	1436	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.4908	403	1436	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.183	381	1436	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	77.8241	332	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,699] [INFO] DFAST Taxonomy check result was written to GCF_003217175.1_ASM321717v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:16,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:16,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:16,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/checkm_data
[2024-01-24 11:52:16,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:16,744] [INFO] Task started: CheckM
[2024-01-24 11:52:16,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217175.1_ASM321717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217175.1_ASM321717v1_genomic.fna/checkm_input GCF_003217175.1_ASM321717v1_genomic.fna/checkm_result
[2024-01-24 11:52:56,592] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:56,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:56,618] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:56,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:56,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217175.1_ASM321717v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:56,620] [INFO] Task started: Blastn
[2024-01-24 11:52:56,620] [INFO] Running command: blastn -query GCF_003217175.1_ASM321717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a2edf8-23eb-48e7-b031-e4e4ff46d075/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217175.1_ASM321717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,015] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,018] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:58,019] [INFO] Target genome list was writen to GCF_003217175.1_ASM321717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,028] [INFO] Task started: fastANI
[2024-01-24 11:52:58,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d0ee21-1235-4d2b-8e35-3764fd3dab36/GCF_003217175.1_ASM321717v1_genomic.fna.gz --refList GCF_003217175.1_ASM321717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217175.1_ASM321717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:06,914] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:06,925] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:53:06,925] [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_002836945.1	s__Shewanella chilikensis	99.9673	1378	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	inconclusive
GCF_002836975.1	s__Shewanella indica	95.7929	1326	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	inconclusive
GCF_009183365.2	s__Shewanella algae	94.482	1316	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002777975.1	s__Shewanella carassii	93.4743	1241	1436	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	78.8628	446	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_003957745.1	s__Shewanella khirikhana	78.5099	478	1436	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	78.4899	315	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018394335.1	s__Shewanella dokdonensis	78.1435	252	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831655.1	s__Shewanella insulae	78.0276	395	1436	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 11:53:06,928] [INFO] GTDB search result was written to GCF_003217175.1_ASM321717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:06,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:06,933] [INFO] DFAST_QC result json was written to GCF_003217175.1_ASM321717v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:06,933] [INFO] DFAST_QC completed!
[2024-01-24 11:53:06,933] [INFO] Total running time: 0h1m17s