[2024-01-25 19:47:20,720] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference
[2024-01-25 19:47:21,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,912] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg78e33391-ec02-4b01-a94e-d9e635e4cceb/GCF_011290685.1_ASM1129068v1_genomic.fna.gz | prodigal -d GCF_011290685.1_ASM1129068v1_genomic.fna/cds.fna -a GCF_011290685.1_ASM1129068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:48,955] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:48,955] [INFO] Task started: HMMsearch
[2024-01-25 19:47:48,956] [INFO] Running command: hmmsearch --tblout GCF_011290685.1_ASM1129068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/reference_markers.hmm GCF_011290685.1_ASM1129068v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:49,258] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:49,259] [INFO] Found 6/6 markers.
[2024-01-25 19:47:49,311] [INFO] Query marker FASTA was written to GCF_011290685.1_ASM1129068v1_genomic.fna/markers.fasta
[2024-01-25 19:47:49,311] [INFO] Task started: Blastn
[2024-01-25 19:47:49,311] [INFO] Running command: blastn -query GCF_011290685.1_ASM1129068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/reference_markers.fasta -out GCF_011290685.1_ASM1129068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:49,899] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:49,901] [INFO] Selected 20 target genomes.
[2024-01-25 19:47:49,902] [INFO] Target genome list was writen to GCF_011290685.1_ASM1129068v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:49,921] [INFO] Task started: fastANI
[2024-01-25 19:47:49,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e33391-ec02-4b01-a94e-d9e635e4cceb/GCF_011290685.1_ASM1129068v1_genomic.fna.gz --refList GCF_011290685.1_ASM1129068v1_genomic.fna/target_genomes.txt --output GCF_011290685.1_ASM1129068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:08,384] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:08,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:08,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:08,395] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:08,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:08,395] [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
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	100.0	2041	2042	95	conclusive
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	81.5911	1125	2042	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	80.3526	758	2042	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	80.0746	735	2042	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	80.0503	772	2042	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	79.1762	573	2042	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	77.3624	319	2042	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	77.3599	306	2042	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	77.0472	103	2042	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	76.7913	182	2042	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	76.7268	90	2042	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.3754	88	2042	95	below_threshold
Lunatimonas lonarensis	strain=AK24	GCA_000390185.1	1232681	1232681	type	True	76.2949	122	2042	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	76.1831	54	2042	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.1803	67	2042	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	75.8523	51	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:08,397] [INFO] DFAST Taxonomy check result was written to GCF_011290685.1_ASM1129068v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:08,397] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:08,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:08,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/checkm_data
[2024-01-25 19:48:08,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:08,456] [INFO] Task started: CheckM
[2024-01-25 19:48:08,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011290685.1_ASM1129068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011290685.1_ASM1129068v1_genomic.fna/checkm_input GCF_011290685.1_ASM1129068v1_genomic.fna/checkm_result
[2024-01-25 19:49:21,613] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:21,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:21,685] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:21,686] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:21,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011290685.1_ASM1129068v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:21,687] [INFO] Task started: Blastn
[2024-01-25 19:49:21,687] [INFO] Running command: blastn -query GCF_011290685.1_ASM1129068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4acf2df6-b62d-40ac-9bf1-bbb6b165e8b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_011290685.1_ASM1129068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:22,501] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:22,506] [INFO] Selected 11 target genomes.
[2024-01-25 19:49:22,506] [INFO] Target genome list was writen to GCF_011290685.1_ASM1129068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:22,516] [INFO] Task started: fastANI
[2024-01-25 19:49:22,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e33391-ec02-4b01-a94e-d9e635e4cceb/GCF_011290685.1_ASM1129068v1_genomic.fna.gz --refList GCF_011290685.1_ASM1129068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011290685.1_ASM1129068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:35,951] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:35,960] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:35,960] [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_011290685.1	s__Cyclobacterium plantarum	100.0	2041	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014762705.1	s__Cyclobacterium sp014762705	94.0976	1658	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	82.5504	1411	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143075.1	s__Cyclobacterium lianum	81.5842	1126	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119245.1	s__Cyclobacterium sp010119245	80.358	756	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119225.1	s__Cyclobacterium sp010119225	80.0721	734	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	80.0611	770	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	79.1839	572	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_000427295.1	s__Cyclobacterium qasimii	77.3599	306	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_002150685.1	s__Algoriphagus antarcticus	75.8523	51	2042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:35,965] [INFO] GTDB search result was written to GCF_011290685.1_ASM1129068v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:35,966] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:35,969] [INFO] DFAST_QC result json was written to GCF_011290685.1_ASM1129068v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:35,969] [INFO] DFAST_QC completed!
[2024-01-25 19:49:35,969] [INFO] Total running time: 0h2m15s