[2024-01-25 20:25:35,406] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:35,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:35,409] [INFO] DQC Reference Directory: /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference
[2024-01-25 20:25:36,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:36,557] [INFO] Task started: Prodigal
[2024-01-25 20:25:36,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e5874e5-69c3-4dcc-af22-be479b6f0698/GCF_021596945.1_ASM2159694v1_genomic.fna.gz | prodigal -d GCF_021596945.1_ASM2159694v1_genomic.fna/cds.fna -a GCF_021596945.1_ASM2159694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:25:55,402] [INFO] Task succeeded: Prodigal
[2024-01-25 20:25:55,402] [INFO] Task started: HMMsearch
[2024-01-25 20:25:55,403] [INFO] Running command: hmmsearch --tblout GCF_021596945.1_ASM2159694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/reference_markers.hmm GCF_021596945.1_ASM2159694v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:25:55,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:25:55,658] [INFO] Found 6/6 markers.
[2024-01-25 20:25:55,694] [INFO] Query marker FASTA was written to GCF_021596945.1_ASM2159694v1_genomic.fna/markers.fasta
[2024-01-25 20:25:55,695] [INFO] Task started: Blastn
[2024-01-25 20:25:55,695] [INFO] Running command: blastn -query GCF_021596945.1_ASM2159694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/reference_markers.fasta -out GCF_021596945.1_ASM2159694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:56,248] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:56,251] [INFO] Selected 18 target genomes.
[2024-01-25 20:25:56,251] [INFO] Target genome list was writen to GCF_021596945.1_ASM2159694v1_genomic.fna/target_genomes.txt
[2024-01-25 20:25:56,283] [INFO] Task started: fastANI
[2024-01-25 20:25:56,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e5874e5-69c3-4dcc-af22-be479b6f0698/GCF_021596945.1_ASM2159694v1_genomic.fna.gz --refList GCF_021596945.1_ASM2159694v1_genomic.fna/target_genomes.txt --output GCF_021596945.1_ASM2159694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:14,019] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:14,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:14,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:14,030] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:14,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:14,030] [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
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	100.0	1605	1605	95	conclusive
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	83.9034	909	1605	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	78.0807	191	1605	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	77.8927	184	1605	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	77.7607	168	1605	95	below_threshold
Echinicola soli	strain=LN3S3	GCA_006575665.1	2591634	2591634	type	True	77.5893	77	1605	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.4875	185	1605	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.3764	182	1605	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	77.3372	86	1605	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.2183	175	1605	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	77.0706	55	1605	95	below_threshold
Pararhodonellum marinum	strain=SW124	GCA_015354735.1	2755358	2755358	type	True	76.9982	97	1605	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.9407	160	1605	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.8176	80	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:14,031] [INFO] DFAST Taxonomy check result was written to GCF_021596945.1_ASM2159694v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:14,032] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:14,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:14,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/checkm_data
[2024-01-25 20:26:14,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:14,080] [INFO] Task started: CheckM
[2024-01-25 20:26:14,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021596945.1_ASM2159694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021596945.1_ASM2159694v1_genomic.fna/checkm_input GCF_021596945.1_ASM2159694v1_genomic.fna/checkm_result
[2024-01-25 20:27:10,454] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:10,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:10,471] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:10,472] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:10,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021596945.1_ASM2159694v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:10,473] [INFO] Task started: Blastn
[2024-01-25 20:27:10,473] [INFO] Running command: blastn -query GCF_021596945.1_ASM2159694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b19c2f-7737-436e-a26b-e0df866c7f71/dqc_reference/reference_markers_gtdb.fasta -out GCF_021596945.1_ASM2159694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:11,260] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:11,262] [INFO] Selected 24 target genomes.
[2024-01-25 20:27:11,263] [INFO] Target genome list was writen to GCF_021596945.1_ASM2159694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:11,296] [INFO] Task started: fastANI
[2024-01-25 20:27:11,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e5874e5-69c3-4dcc-af22-be479b6f0698/GCF_021596945.1_ASM2159694v1_genomic.fna.gz --refList GCF_021596945.1_ASM2159694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021596945.1_ASM2159694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:30,415] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:30,428] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:27:30,428] [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_014652135.1	s__Mongoliitalea lutea	83.8865	910	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	78.8021	228	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	78.1705	230	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	78.1508	192	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	77.8395	207	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	77.8259	188	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.7611	207	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	77.5947	193	1605	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	77.4709	186	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	77.429	76	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.3372	86	1605	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	77.2081	176	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	77.2003	104	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354735.1	s__SW124 sp015354735	76.9982	98	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.9261	160	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.9258	87	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.8224	164	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	76.8171	99	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:30,430] [INFO] GTDB search result was written to GCF_021596945.1_ASM2159694v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:30,430] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:30,434] [INFO] DFAST_QC result json was written to GCF_021596945.1_ASM2159694v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:30,434] [INFO] DFAST_QC completed!
[2024-01-25 20:27:30,434] [INFO] Total running time: 0h1m55s