[2024-01-24 14:05:34,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference
[2024-01-24 14:05:35,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,452] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg251a707a-f4ac-4b75-87f7-9246255dbbe6/GCF_013283795.1_ASM1328379v1_genomic.fna.gz | prodigal -d GCF_013283795.1_ASM1328379v1_genomic.fna/cds.fna -a GCF_013283795.1_ASM1328379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,677] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,677] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,677] [INFO] Running command: hmmsearch --tblout GCF_013283795.1_ASM1328379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/reference_markers.hmm GCF_013283795.1_ASM1328379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:45,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:45,989] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,024] [INFO] Query marker FASTA was written to GCF_013283795.1_ASM1328379v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,025] [INFO] Task started: Blastn
[2024-01-24 14:05:46,025] [INFO] Running command: blastn -query GCF_013283795.1_ASM1328379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/reference_markers.fasta -out GCF_013283795.1_ASM1328379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:46,835] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:46,842] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:46,843] [INFO] Target genome list was writen to GCF_013283795.1_ASM1328379v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:46,855] [INFO] Task started: fastANI
[2024-01-24 14:05:46,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg251a707a-f4ac-4b75-87f7-9246255dbbe6/GCF_013283795.1_ASM1328379v1_genomic.fna.gz --refList GCF_013283795.1_ASM1328379v1_genomic.fna/target_genomes.txt --output GCF_013283795.1_ASM1328379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:56,727] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:56,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:56,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:56,738] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:56,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:56,738] [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
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	100.0	1339	1342	95	conclusive
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	83.6591	780	1342	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	83.6305	793	1342	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	82.9352	913	1342	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	82.8124	918	1342	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	81.8617	801	1342	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	81.3137	750	1342	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	80.6221	603	1342	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	78.3237	342	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:56,740] [INFO] DFAST Taxonomy check result was written to GCF_013283795.1_ASM1328379v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:56,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:56,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:56,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/checkm_data
[2024-01-24 14:05:56,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:56,783] [INFO] Task started: CheckM
[2024-01-24 14:05:56,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283795.1_ASM1328379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283795.1_ASM1328379v1_genomic.fna/checkm_input GCF_013283795.1_ASM1328379v1_genomic.fna/checkm_result
[2024-01-24 14:06:30,585] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:30,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:30,603] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:30,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:30,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283795.1_ASM1328379v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:30,604] [INFO] Task started: Blastn
[2024-01-24 14:06:30,604] [INFO] Running command: blastn -query GCF_013283795.1_ASM1328379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a93ec7-cae8-4373-811e-2ffa16e51fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283795.1_ASM1328379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,929] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,932] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:31,932] [INFO] Target genome list was writen to GCF_013283795.1_ASM1328379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:31,962] [INFO] Task started: fastANI
[2024-01-24 14:06:31,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg251a707a-f4ac-4b75-87f7-9246255dbbe6/GCF_013283795.1_ASM1328379v1_genomic.fna.gz --refList GCF_013283795.1_ASM1328379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283795.1_ASM1328379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:44,384] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:44,394] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:44,395] [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_013283795.1	s__Rheinheimera sp013283795	100.0	1339	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017824735.1	s__Rheinheimera sp017824735	83.6588	780	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001513785.1	s__Rheinheimera sp001513785	83.0407	942	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	82.9249	938	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	82.8178	916	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	82.3974	808	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCA_018831085.1	s__Rheinheimera sp018831085	82.3277	909	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011634895.1	s__Rheinheimera pleomorphica	81.8617	801	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	81.3082	750	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425345.1	s__Rheinheimera baltica	80.6362	601	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245735.1	s__Alishewanella jeotgali	78.3227	340	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,396] [INFO] GTDB search result was written to GCF_013283795.1_ASM1328379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:44,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:44,400] [INFO] DFAST_QC result json was written to GCF_013283795.1_ASM1328379v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:44,400] [INFO] DFAST_QC completed!
[2024-01-24 14:06:44,400] [INFO] Total running time: 0h1m10s