[2024-01-24 12:31:04,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference
[2024-01-24 12:31:05,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,659] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9572f2c-672f-4689-9d3f-a9c2f3eb4f29/GCF_000473765.1_Rpsyc1.0_genomic.fna.gz | prodigal -d GCF_000473765.1_Rpsyc1.0_genomic.fna/cds.fna -a GCF_000473765.1_Rpsyc1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:34,248] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:34,248] [INFO] Task started: HMMsearch
[2024-01-24 12:31:34,249] [INFO] Running command: hmmsearch --tblout GCF_000473765.1_Rpsyc1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/reference_markers.hmm GCF_000473765.1_Rpsyc1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:34,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:34,566] [INFO] Found 6/6 markers.
[2024-01-24 12:31:34,615] [INFO] Query marker FASTA was written to GCF_000473765.1_Rpsyc1.0_genomic.fna/markers.fasta
[2024-01-24 12:31:34,615] [INFO] Task started: Blastn
[2024-01-24 12:31:34,615] [INFO] Running command: blastn -query GCF_000473765.1_Rpsyc1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/reference_markers.fasta -out GCF_000473765.1_Rpsyc1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:35,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:35,217] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:35,218] [INFO] Target genome list was writen to GCF_000473765.1_Rpsyc1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:31:35,226] [INFO] Task started: fastANI
[2024-01-24 12:31:35,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9572f2c-672f-4689-9d3f-a9c2f3eb4f29/GCF_000473765.1_Rpsyc1.0_genomic.fna.gz --refList GCF_000473765.1_Rpsyc1.0_genomic.fna/target_genomes.txt --output GCF_000473765.1_Rpsyc1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:48,087] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:48,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:48,108] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:48,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:48,109] [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
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	100.0	1611	1621	95	conclusive
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	99.9993	1621	1621	95	conclusive
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	77.1755	150	1621	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.0745	179	1621	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.066	180	1621	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.0584	169	1621	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	76.8974	153	1621	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	76.6392	164	1621	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	76.4685	218	1621	95	below_threshold
Litoribacter populi	strain=XAAS-A1	GCA_007483685.1	2598460	2598460	type	True	76.359	104	1621	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.2828	95	1621	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.2223	128	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,111] [INFO] DFAST Taxonomy check result was written to GCF_000473765.1_Rpsyc1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:31:48,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:48,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:48,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/checkm_data
[2024-01-24 12:31:48,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:48,167] [INFO] Task started: CheckM
[2024-01-24 12:31:48,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000473765.1_Rpsyc1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000473765.1_Rpsyc1.0_genomic.fna/checkm_input GCF_000473765.1_Rpsyc1.0_genomic.fna/checkm_result
[2024-01-24 12:33:08,835] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:08,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,859] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:08,859] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:08,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000473765.1_Rpsyc1.0_genomic.fna/markers.fasta)
[2024-01-24 12:33:08,860] [INFO] Task started: Blastn
[2024-01-24 12:33:08,860] [INFO] Running command: blastn -query GCF_000473765.1_Rpsyc1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a69a00-4012-48d2-a640-956f0473c861/dqc_reference/reference_markers_gtdb.fasta -out GCF_000473765.1_Rpsyc1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:09,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:09,648] [INFO] Selected 21 target genomes.
[2024-01-24 12:33:09,648] [INFO] Target genome list was writen to GCF_000473765.1_Rpsyc1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:09,663] [INFO] Task started: fastANI
[2024-01-24 12:33:09,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9572f2c-672f-4689-9d3f-a9c2f3eb4f29/GCF_000473765.1_Rpsyc1.0_genomic.fna.gz --refList GCF_000473765.1_Rpsyc1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000473765.1_Rpsyc1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:23,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:23,629] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:23,630] [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_000381545.1	s__Rhodonellum psychrophilum	99.9993	1621	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_900156785.1	s__Belliella pelovolcani	77.1755	150	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.066	180	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	77.0584	169	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	76.9149	151	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.6392	164	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.6383	227	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	76.595	163	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.5938	212	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.5353	69	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.4685	218	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.3924	169	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	76.3684	129	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_007483685.1	s__Litoribacter sp007483685	76.359	104	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	76.2828	95	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	76.1519	111	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_017254915.1	s__Algoriphagus sp017254915	76.0903	80	1621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:23,631] [INFO] GTDB search result was written to GCF_000473765.1_Rpsyc1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:23,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:23,639] [INFO] DFAST_QC result json was written to GCF_000473765.1_Rpsyc1.0_genomic.fna/dqc_result.json
[2024-01-24 12:33:23,640] [INFO] DFAST_QC completed!
[2024-01-24 12:33:23,640] [INFO] Total running time: 0h2m19s