[2024-01-25 17:42:20,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference
[2024-01-25 17:42:21,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,623] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,624] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaa542ff-b17a-48ff-8aed-c1ba85902c8b/GCF_016798325.1_ASM1679832v1_genomic.fna.gz | prodigal -d GCF_016798325.1_ASM1679832v1_genomic.fna/cds.fna -a GCF_016798325.1_ASM1679832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:33,861] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:33,861] [INFO] Task started: HMMsearch
[2024-01-25 17:42:33,861] [INFO] Running command: hmmsearch --tblout GCF_016798325.1_ASM1679832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/reference_markers.hmm GCF_016798325.1_ASM1679832v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:34,109] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:34,110] [INFO] Found 6/6 markers.
[2024-01-25 17:42:34,147] [INFO] Query marker FASTA was written to GCF_016798325.1_ASM1679832v1_genomic.fna/markers.fasta
[2024-01-25 17:42:34,147] [INFO] Task started: Blastn
[2024-01-25 17:42:34,147] [INFO] Running command: blastn -query GCF_016798325.1_ASM1679832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/reference_markers.fasta -out GCF_016798325.1_ASM1679832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:35,021] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:35,024] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:35,025] [INFO] Target genome list was writen to GCF_016798325.1_ASM1679832v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:35,083] [INFO] Task started: fastANI
[2024-01-25 17:42:35,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa542ff-b17a-48ff-8aed-c1ba85902c8b/GCF_016798325.1_ASM1679832v1_genomic.fna.gz --refList GCF_016798325.1_ASM1679832v1_genomic.fna/target_genomes.txt --output GCF_016798325.1_ASM1679832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:46,217] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:46,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:46,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:46,225] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:46,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:46,225] [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
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	100.0	1540	1542	95	conclusive
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	88.0601	1243	1542	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	82.1706	1041	1542	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	80.037	800	1542	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	79.6791	660	1542	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.9344	462	1542	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.783	500	1542	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.6741	384	1542	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.5413	375	1542	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.0834	372	1542	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	78.0592	358	1542	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	77.7093	288	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:46,227] [INFO] DFAST Taxonomy check result was written to GCF_016798325.1_ASM1679832v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:46,227] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:46,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:46,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/checkm_data
[2024-01-25 17:42:46,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:46,271] [INFO] Task started: CheckM
[2024-01-25 17:42:46,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016798325.1_ASM1679832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016798325.1_ASM1679832v1_genomic.fna/checkm_input GCF_016798325.1_ASM1679832v1_genomic.fna/checkm_result
[2024-01-25 17:43:23,596] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:23,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:23,630] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:23,631] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:23,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016798325.1_ASM1679832v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:23,631] [INFO] Task started: Blastn
[2024-01-25 17:43:23,631] [INFO] Running command: blastn -query GCF_016798325.1_ASM1679832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg741da54c-c4b3-4b3f-8523-48b0d6abbead/dqc_reference/reference_markers_gtdb.fasta -out GCF_016798325.1_ASM1679832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:25,211] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:25,214] [INFO] Selected 8 target genomes.
[2024-01-25 17:43:25,214] [INFO] Target genome list was writen to GCF_016798325.1_ASM1679832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:25,224] [INFO] Task started: fastANI
[2024-01-25 17:43:25,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa542ff-b17a-48ff-8aed-c1ba85902c8b/GCF_016798325.1_ASM1679832v1_genomic.fna.gz --refList GCF_016798325.1_ASM1679832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016798325.1_ASM1679832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:33,968] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:33,975] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:33,975] [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_003789045.1	s__Marinobacter_A sp003789045	97.6714	1374	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	conclusive
GCF_004327985.1	s__Marinobacter_A halodurans	88.0538	1244	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	82.1612	1043	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	80.0477	798	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122265.1	s__Marinobacter_A fonticola	79.6834	659	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	78.9395	461	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.5716	445	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	78.2813	364	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:33,976] [INFO] GTDB search result was written to GCF_016798325.1_ASM1679832v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:33,977] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:33,979] [INFO] DFAST_QC result json was written to GCF_016798325.1_ASM1679832v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:33,979] [INFO] DFAST_QC completed!
[2024-01-25 17:43:33,979] [INFO] Total running time: 0h1m13s