[2023-06-18 11:44:48,129] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:48,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:48,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference
[2023-06-18 11:44:49,427] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:49,428] [INFO] Task started: Prodigal
[2023-06-18 11:44:49,429] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dd0f993-b54f-4106-b99c-c99cd727add9/GCA_018003815.1_ASM1800381v1_genomic.fna.gz | prodigal -d GCA_018003815.1_ASM1800381v1_genomic.fna/cds.fna -a GCA_018003815.1_ASM1800381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:44:52,166] [INFO] Task succeeded: Prodigal
[2023-06-18 11:44:52,166] [INFO] Task started: HMMsearch
[2023-06-18 11:44:52,166] [INFO] Running command: hmmsearch --tblout GCA_018003815.1_ASM1800381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/reference_markers.hmm GCA_018003815.1_ASM1800381v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:44:52,357] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:44:52,359] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4dd0f993-b54f-4106-b99c-c99cd727add9/GCA_018003815.1_ASM1800381v1_genomic.fna.gz]
[2023-06-18 11:44:52,378] [INFO] Query marker FASTA was written to GCA_018003815.1_ASM1800381v1_genomic.fna/markers.fasta
[2023-06-18 11:44:52,379] [INFO] Task started: Blastn
[2023-06-18 11:44:52,379] [INFO] Running command: blastn -query GCA_018003815.1_ASM1800381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/reference_markers.fasta -out GCA_018003815.1_ASM1800381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:44:53,640] [INFO] Task succeeded: Blastn
[2023-06-18 11:44:53,644] [INFO] Selected 8 target genomes.
[2023-06-18 11:44:53,644] [INFO] Target genome list was writen to GCA_018003815.1_ASM1800381v1_genomic.fna/target_genomes.txt
[2023-06-18 11:44:53,685] [INFO] Task started: fastANI
[2023-06-18 11:44:53,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd0f993-b54f-4106-b99c-c99cd727add9/GCA_018003815.1_ASM1800381v1_genomic.fna.gz --refList GCA_018003815.1_ASM1800381v1_genomic.fna/target_genomes.txt --output GCA_018003815.1_ASM1800381v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:44:57,026] [INFO] Task succeeded: fastANI
[2023-06-18 11:44:57,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:44:57,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:44:57,034] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:44:57,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:44:57,035] [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	86.4282	133	159	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	86.4282	133	159	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	78.3967	72	159	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	78.2526	63	159	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	77.4099	54	159	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	76.7462	57	159	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	76.7462	57	159	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:44:57,037] [INFO] DFAST Taxonomy check result was written to GCA_018003815.1_ASM1800381v1_genomic.fna/tc_result.tsv
[2023-06-18 11:44:57,037] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:44:57,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:44:57,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/checkm_data
[2023-06-18 11:44:57,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:44:57,064] [INFO] Task started: CheckM
[2023-06-18 11:44:57,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018003815.1_ASM1800381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018003815.1_ASM1800381v1_genomic.fna/checkm_input GCA_018003815.1_ASM1800381v1_genomic.fna/checkm_result
[2023-06-18 11:45:13,145] [INFO] Task succeeded: CheckM
[2023-06-18 11:45:13,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 14.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:45:13,177] [INFO] ===== Completeness check finished =====
[2023-06-18 11:45:13,178] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:45:13,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018003815.1_ASM1800381v1_genomic.fna/markers.fasta)
[2023-06-18 11:45:13,179] [INFO] Task started: Blastn
[2023-06-18 11:45:13,179] [INFO] Running command: blastn -query GCA_018003815.1_ASM1800381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2403db9a-a8d5-4428-915c-836adaaacbda/dqc_reference/reference_markers_gtdb.fasta -out GCA_018003815.1_ASM1800381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:13,883] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:13,888] [INFO] Selected 6 target genomes.
[2023-06-18 11:45:13,888] [INFO] Target genome list was writen to GCA_018003815.1_ASM1800381v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:45:13,893] [INFO] Task started: fastANI
[2023-06-18 11:45:13,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd0f993-b54f-4106-b99c-c99cd727add9/GCA_018003815.1_ASM1800381v1_genomic.fna.gz --refList GCA_018003815.1_ASM1800381v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018003815.1_ASM1800381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:45:16,328] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:16,334] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 11:45:16,335] [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_002205795.1	s__Kaistella sp002205795	87.4542	145	159	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCF_019195395.1	s__Kaistella sp019195395	86.4282	133	159	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453895.1	s__Kaistella sp002453895	86.2134	136	159	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	84.5733	136	159	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCA_002197835.1	s__Kaistella sp002197835	79.8349	112	159	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	79.7833	111	159	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:45:16,336] [INFO] GTDB search result was written to GCA_018003815.1_ASM1800381v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:45:16,337] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:45:16,340] [INFO] DFAST_QC result json was written to GCA_018003815.1_ASM1800381v1_genomic.fna/dqc_result.json
[2023-06-18 11:45:16,340] [INFO] DFAST_QC completed!
[2023-06-18 11:45:16,340] [INFO] Total running time: 0h0m28s