[2023-06-28 10:15:47,107] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:15:47,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:15:47,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference
[2023-06-28 10:15:48,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:15:48,307] [INFO] Task started: Prodigal
[2023-06-28 10:15:48,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ce58c6f-178e-4c71-8cda-318374b4338d/GCA_017554485.1_ASM1755448v1_genomic.fna.gz | prodigal -d GCA_017554485.1_ASM1755448v1_genomic.fna/cds.fna -a GCA_017554485.1_ASM1755448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:15:55,165] [INFO] Task succeeded: Prodigal
[2023-06-28 10:15:55,165] [INFO] Task started: HMMsearch
[2023-06-28 10:15:55,166] [INFO] Running command: hmmsearch --tblout GCA_017554485.1_ASM1755448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/reference_markers.hmm GCA_017554485.1_ASM1755448v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:15:55,422] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:15:55,424] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ce58c6f-178e-4c71-8cda-318374b4338d/GCA_017554485.1_ASM1755448v1_genomic.fna.gz]
[2023-06-28 10:15:55,453] [INFO] Query marker FASTA was written to GCA_017554485.1_ASM1755448v1_genomic.fna/markers.fasta
[2023-06-28 10:15:55,454] [INFO] Task started: Blastn
[2023-06-28 10:15:55,454] [INFO] Running command: blastn -query GCA_017554485.1_ASM1755448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/reference_markers.fasta -out GCA_017554485.1_ASM1755448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:15:56,078] [INFO] Task succeeded: Blastn
[2023-06-28 10:15:56,082] [INFO] Selected 23 target genomes.
[2023-06-28 10:15:56,083] [INFO] Target genome list was writen to GCA_017554485.1_ASM1755448v1_genomic.fna/target_genomes.txt
[2023-06-28 10:15:56,087] [INFO] Task started: fastANI
[2023-06-28 10:15:56,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce58c6f-178e-4c71-8cda-318374b4338d/GCA_017554485.1_ASM1755448v1_genomic.fna.gz --refList GCA_017554485.1_ASM1755448v1_genomic.fna/target_genomes.txt --output GCA_017554485.1_ASM1755448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:09,191] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:09,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:09,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:09,199] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:09,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:16:09,199] [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
Succiniclasticum ruminis	strain=DSM 9236	GCA_900112895.1	40841	40841	suspected-type	True	82.3085	441	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:16:09,201] [INFO] DFAST Taxonomy check result was written to GCA_017554485.1_ASM1755448v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:09,202] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:09,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:09,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/checkm_data
[2023-06-28 10:16:09,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:09,236] [INFO] Task started: CheckM
[2023-06-28 10:16:09,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017554485.1_ASM1755448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017554485.1_ASM1755448v1_genomic.fna/checkm_input GCA_017554485.1_ASM1755448v1_genomic.fna/checkm_result
[2023-06-28 10:16:35,840] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:35,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:35,863] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:35,864] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:35,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017554485.1_ASM1755448v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:35,865] [INFO] Task started: Blastn
[2023-06-28 10:16:35,865] [INFO] Running command: blastn -query GCA_017554485.1_ASM1755448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bca14fe-9927-4a2c-8251-04cd5d94979b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017554485.1_ASM1755448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:36,812] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:36,817] [INFO] Selected 13 target genomes.
[2023-06-28 10:16:36,817] [INFO] Target genome list was writen to GCA_017554485.1_ASM1755448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:36,820] [INFO] Task started: fastANI
[2023-06-28 10:16:36,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce58c6f-178e-4c71-8cda-318374b4338d/GCA_017554485.1_ASM1755448v1_genomic.fna.gz --refList GCA_017554485.1_ASM1755448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017554485.1_ASM1755448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:16:42,434] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:42,449] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:16:42,450] [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
GCA_017554485.1	s__Succiniclasticum sp017554485	100.0	754	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905233365.1	s__Succiniclasticum sp905233365	82.7789	420	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.76	98.76	0.84	0.84	2	-
GCA_902801365.1	s__Succiniclasticum sp902801365	82.5195	408	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.72	97.62	0.82	0.80	3	-
GCA_017405945.1	s__Succiniclasticum sp017405945	82.4243	427	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112895.1	s__Succiniclasticum ruminis	82.3215	439	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315925.1	s__Succiniclasticum sp900315925	82.0515	438	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	96.41	95.14	0.84	0.70	42	-
GCA_017443165.1	s__Succiniclasticum sp017443165	81.7266	239	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003512125.1	s__Succiniclasticum sp003512125	80.9938	262	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.84	98.84	0.85	0.85	2	-
GCA_017460905.1	s__Succiniclasticum sp017460905	80.5384	292	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.67	97.67	0.73	0.73	2	-
GCA_002342505.1	s__Succiniclasticum sp002342505	79.6824	271	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.62	97.51	0.81	0.72	6	-
GCA_900316935.1	s__Succiniclasticum sp900316935	77.3021	113	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	99.76	99.29	0.95	0.93	11	-
--------------------------------------------------------------------------------
[2023-06-28 10:16:42,452] [INFO] GTDB search result was written to GCA_017554485.1_ASM1755448v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:16:42,452] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:16:42,455] [INFO] DFAST_QC result json was written to GCA_017554485.1_ASM1755448v1_genomic.fna/dqc_result.json
[2023-06-28 10:16:42,455] [INFO] DFAST_QC completed!
[2023-06-28 10:16:42,455] [INFO] Total running time: 0h0m55s