[2024-01-25 18:44:35,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference
[2024-01-25 18:44:36,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,809] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg51ae8265-9fdc-44f7-98bc-ea1353efe046/GCF_024813435.1_ASM2481343v1_genomic.fna.gz | prodigal -d GCF_024813435.1_ASM2481343v1_genomic.fna/cds.fna -a GCF_024813435.1_ASM2481343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:58,688] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:58,688] [INFO] Task started: HMMsearch
[2024-01-25 18:44:58,688] [INFO] Running command: hmmsearch --tblout GCF_024813435.1_ASM2481343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/reference_markers.hmm GCF_024813435.1_ASM2481343v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:58,947] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:58,948] [INFO] Found 6/6 markers.
[2024-01-25 18:44:58,990] [INFO] Query marker FASTA was written to GCF_024813435.1_ASM2481343v1_genomic.fna/markers.fasta
[2024-01-25 18:44:58,990] [INFO] Task started: Blastn
[2024-01-25 18:44:58,990] [INFO] Running command: blastn -query GCF_024813435.1_ASM2481343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/reference_markers.fasta -out GCF_024813435.1_ASM2481343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:59,554] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:59,557] [INFO] Selected 20 target genomes.
[2024-01-25 18:44:59,557] [INFO] Target genome list was writen to GCF_024813435.1_ASM2481343v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:59,574] [INFO] Task started: fastANI
[2024-01-25 18:44:59,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ae8265-9fdc-44f7-98bc-ea1353efe046/GCF_024813435.1_ASM2481343v1_genomic.fna.gz --refList GCF_024813435.1_ASM2481343v1_genomic.fna/target_genomes.txt --output GCF_024813435.1_ASM2481343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:16,503] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:16,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:16,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:16,515] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:16,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:16,516] [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
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	86.9663	1276	1693	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	78.0028	469	1693	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.8136	433	1693	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.8333	281	1693	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.8175	161	1693	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	76.7846	251	1693	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.7573	160	1693	95	below_threshold
Pararhodonellum marinum	strain=SW124	GCA_015354735.1	2755358	2755358	type	True	76.7447	140	1693	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.7337	204	1693	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.6098	119	1693	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.5191	102	1693	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.3664	105	1693	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	76.3493	100	1693	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	76.2536	100	1693	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.2431	89	1693	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	76.2184	99	1693	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	76.2102	111	1693	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.1242	121	1693	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	75.9276	93	1693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:16,517] [INFO] DFAST Taxonomy check result was written to GCF_024813435.1_ASM2481343v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:16,517] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:16,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:16,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/checkm_data
[2024-01-25 18:45:16,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:16,567] [INFO] Task started: CheckM
[2024-01-25 18:45:16,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024813435.1_ASM2481343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024813435.1_ASM2481343v1_genomic.fna/checkm_input GCF_024813435.1_ASM2481343v1_genomic.fna/checkm_result
[2024-01-25 18:46:19,804] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:19,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:19,818] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:19,818] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:19,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024813435.1_ASM2481343v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:19,820] [INFO] Task started: Blastn
[2024-01-25 18:46:19,820] [INFO] Running command: blastn -query GCF_024813435.1_ASM2481343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b6c4ec0-4dad-4136-9292-7bcb642e1b06/dqc_reference/reference_markers_gtdb.fasta -out GCF_024813435.1_ASM2481343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:20,617] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:20,620] [INFO] Selected 21 target genomes.
[2024-01-25 18:46:20,620] [INFO] Target genome list was writen to GCF_024813435.1_ASM2481343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:20,636] [INFO] Task started: fastANI
[2024-01-25 18:46:20,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ae8265-9fdc-44f7-98bc-ea1353efe046/GCF_024813435.1_ASM2481343v1_genomic.fna.gz --refList GCF_024813435.1_ASM2481343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024813435.1_ASM2481343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:37,905] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:37,918] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:46:37,918] [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_003316845.1	s__Aquiflexum_A aquatile	86.9468	1278	1693	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_900176595.1	s__Aquiflexum balticum	78.0204	466	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	77.8144	433	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.0453	180	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_003003005.1	s__Mongoliibacter ruber	76.9662	237	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	76.8333	281	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.8175	161	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.7846	251	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.7477	223	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.7449	203	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354735.1	s__SW124 sp015354735	76.7447	140	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	76.6845	90	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	76.5301	135	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	76.5191	102	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.3706	106	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.3284	223	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.2536	100	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429465.1	s__Algoriphagus vanfongensis	76.2267	100	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373335.1	s__Algoriphagus sp013373335	76.0821	70	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	75.9435	92	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373065.1	s__Algoriphagus sp013373065	75.6741	97	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:37,920] [INFO] GTDB search result was written to GCF_024813435.1_ASM2481343v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:37,920] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:37,924] [INFO] DFAST_QC result json was written to GCF_024813435.1_ASM2481343v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:37,924] [INFO] DFAST_QC completed!
[2024-01-25 18:46:37,924] [INFO] Total running time: 0h2m2s