[2024-01-24 12:31:56,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:56,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:56,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference
[2024-01-24 12:31:58,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,128] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg099aa5f2-d7f2-4b86-9c0b-e88a9b97bca2/GCF_020985365.1_ASM2098536v1_genomic.fna.gz | prodigal -d GCF_020985365.1_ASM2098536v1_genomic.fna/cds.fna -a GCF_020985365.1_ASM2098536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:08,818] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:08,818] [INFO] Task started: HMMsearch
[2024-01-24 12:32:08,818] [INFO] Running command: hmmsearch --tblout GCF_020985365.1_ASM2098536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/reference_markers.hmm GCF_020985365.1_ASM2098536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:09,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:09,115] [INFO] Found 6/6 markers.
[2024-01-24 12:32:09,154] [INFO] Query marker FASTA was written to GCF_020985365.1_ASM2098536v1_genomic.fna/markers.fasta
[2024-01-24 12:32:09,155] [INFO] Task started: Blastn
[2024-01-24 12:32:09,155] [INFO] Running command: blastn -query GCF_020985365.1_ASM2098536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/reference_markers.fasta -out GCF_020985365.1_ASM2098536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,840] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:09,840] [INFO] Target genome list was writen to GCF_020985365.1_ASM2098536v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,848] [INFO] Task started: fastANI
[2024-01-24 12:32:09,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg099aa5f2-d7f2-4b86-9c0b-e88a9b97bca2/GCF_020985365.1_ASM2098536v1_genomic.fna.gz --refList GCF_020985365.1_ASM2098536v1_genomic.fna/target_genomes.txt --output GCF_020985365.1_ASM2098536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:20,148] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:20,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:20,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:20,163] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:20,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:20,164] [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
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	100.0	886	886	95	conclusive
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	99.9992	886	886	95	conclusive
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	78.3876	292	886	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	78.3618	319	886	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	78.3357	354	886	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.306	349	886	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	78.2421	341	886	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	78.2034	311	886	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.0103	285	886	95	below_threshold
Epilithonimonas mollis	strain=DSM 18016	GCA_900142325.1	216903	216903	type	True	77.7317	131	886	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	77.7127	262	886	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	77.6298	262	886	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	77.3816	163	886	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	77.3409	174	886	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.319	184	886	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	77.2476	172	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,166] [INFO] DFAST Taxonomy check result was written to GCF_020985365.1_ASM2098536v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:20,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:20,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:20,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/checkm_data
[2024-01-24 12:32:20,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:20,200] [INFO] Task started: CheckM
[2024-01-24 12:32:20,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020985365.1_ASM2098536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020985365.1_ASM2098536v1_genomic.fna/checkm_input GCF_020985365.1_ASM2098536v1_genomic.fna/checkm_result
[2024-01-24 12:32:56,507] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:56,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:56,538] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:56,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:56,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020985365.1_ASM2098536v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:56,540] [INFO] Task started: Blastn
[2024-01-24 12:32:56,540] [INFO] Running command: blastn -query GCF_020985365.1_ASM2098536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c5c310-dd2a-4ee8-9298-5bfa86ba7fc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_020985365.1_ASM2098536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:57,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:57,475] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:57,476] [INFO] Target genome list was writen to GCF_020985365.1_ASM2098536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:57,485] [INFO] Task started: fastANI
[2024-01-24 12:32:57,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg099aa5f2-d7f2-4b86-9c0b-e88a9b97bca2/GCF_020985365.1_ASM2098536v1_genomic.fna.gz --refList GCF_020985365.1_ASM2098536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020985365.1_ASM2098536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:02,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:02,537] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:02,538] [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_019195395.1	s__Kaistella sp019195395	99.9992	886	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002453895.1	s__Kaistella sp002453895	94.2123	769	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015999765.1	s__Kaistella sp015999765	93.4651	766	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_002205795.1	s__Kaistella sp002205795	83.6461	666	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCA_002197835.1	s__Kaistella sp002197835	82.3619	585	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCA_018902795.1	s__Kaistella sp018902795	81.3788	575	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735695.2	s__Kaistella haifensis	80.4123	406	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCF_008014695.1	s__Kaistella sp008014695	78.4906	305	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:02,540] [INFO] GTDB search result was written to GCF_020985365.1_ASM2098536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:02,541] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:02,545] [INFO] DFAST_QC result json was written to GCF_020985365.1_ASM2098536v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:02,545] [INFO] DFAST_QC completed!
[2024-01-24 12:33:02,545] [INFO] Total running time: 0h1m6s