[2023-06-28 10:22:07,837] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference
[2023-06-28 10:22:10,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,400] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5dee6c4-6ba2-4f03-8e18-24b2bf8c68ba/GCA_002492425.1_ASM249242v1_genomic.fna.gz | prodigal -d GCA_002492425.1_ASM249242v1_genomic.fna/cds.fna -a GCA_002492425.1_ASM249242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:16,256] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:16,257] [INFO] Task started: HMMsearch
[2023-06-28 10:22:16,257] [INFO] Running command: hmmsearch --tblout GCA_002492425.1_ASM249242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/reference_markers.hmm GCA_002492425.1_ASM249242v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:16,510] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:16,511] [INFO] Found 6/6 markers.
[2023-06-28 10:22:16,541] [INFO] Query marker FASTA was written to GCA_002492425.1_ASM249242v1_genomic.fna/markers.fasta
[2023-06-28 10:22:16,542] [INFO] Task started: Blastn
[2023-06-28 10:22:16,542] [INFO] Running command: blastn -query GCA_002492425.1_ASM249242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/reference_markers.fasta -out GCA_002492425.1_ASM249242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:17,276] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:17,280] [INFO] Selected 26 target genomes.
[2023-06-28 10:22:17,280] [INFO] Target genome list was writen to GCA_002492425.1_ASM249242v1_genomic.fna/target_genomes.txt
[2023-06-28 10:22:17,283] [INFO] Task started: fastANI
[2023-06-28 10:22:17,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5dee6c4-6ba2-4f03-8e18-24b2bf8c68ba/GCA_002492425.1_ASM249242v1_genomic.fna.gz --refList GCA_002492425.1_ASM249242v1_genomic.fna/target_genomes.txt --output GCA_002492425.1_ASM249242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:33,641] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:33,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:33,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:33,649] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 10:22:33,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 10:22:33,650] [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
Frisingicoccus caecimuris	strain=DSM 28559	GCA_004340975.1	1796636	1796636	type	True	98.444	665	739	95	conclusive
Frisingicoccus caecimuris	strain=DSM 28559	GCA_024622585.1	1796636	1796636	type	True	98.4301	666	739	95	conclusive
Coprococcus catus	strain=VPIC661	GCA_019734885.1	116085	116085	suspected-type	True	76.9804	88	739	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	76.9172	91	739	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.8269	50	739	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:33,652] [INFO] DFAST Taxonomy check result was written to GCA_002492425.1_ASM249242v1_genomic.fna/tc_result.tsv
[2023-06-28 10:22:33,653] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:33,653] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:33,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/checkm_data
[2023-06-28 10:22:33,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:33,682] [INFO] Task started: CheckM
[2023-06-28 10:22:33,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002492425.1_ASM249242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002492425.1_ASM249242v1_genomic.fna/checkm_input GCA_002492425.1_ASM249242v1_genomic.fna/checkm_result
[2023-06-28 10:22:57,566] [INFO] Task succeeded: CheckM
[2023-06-28 10:22:57,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:22:57,592] [INFO] ===== Completeness check finished =====
[2023-06-28 10:22:57,593] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:22:57,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002492425.1_ASM249242v1_genomic.fna/markers.fasta)
[2023-06-28 10:22:57,594] [INFO] Task started: Blastn
[2023-06-28 10:22:57,594] [INFO] Running command: blastn -query GCA_002492425.1_ASM249242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c9cf47-f19d-428d-95a0-d641c43dbd8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002492425.1_ASM249242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:58,659] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:58,664] [INFO] Selected 16 target genomes.
[2023-06-28 10:22:58,665] [INFO] Target genome list was writen to GCA_002492425.1_ASM249242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:22:58,674] [INFO] Task started: fastANI
[2023-06-28 10:22:58,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5dee6c4-6ba2-4f03-8e18-24b2bf8c68ba/GCA_002492425.1_ASM249242v1_genomic.fna.gz --refList GCA_002492425.1_ASM249242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002492425.1_ASM249242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:23:05,936] [INFO] Task succeeded: fastANI
[2023-06-28 10:23:05,949] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:23:05,950] [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_004340975.1	s__Frisingicoccus caecimuris	98.444	665	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	98.08	97.54	0.83	0.77	6	conclusive
GCA_900549105.1	s__Frisingicoccus sp900549105	82.4998	466	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.93	99.87	0.93	0.90	3	-
GCA_900753685.1	s__Frisingicoccus sp900753685	82.1763	358	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.11	98.62	0.83	0.76	3	-
GCA_016298055.1	s__Frisingicoccus sp016298055	79.583	250	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	95.75	95.75	0.73	0.73	2	-
GCA_900757195.1	s__Frisingicoccus sp900757195	79.0889	300	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.09	99.09	0.92	0.92	2	-
GCA_009929615.1	s__Frisingicoccus sp009929615	78.8316	280	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	-
GCA_017391465.1	s__Frisingicoccus sp017391465	78.1728	161	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711005.1	s__Catenibacillus faecigallinarum	77.0444	66	739	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.82	99.82	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:23:05,952] [INFO] GTDB search result was written to GCA_002492425.1_ASM249242v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:23:05,953] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:23:05,955] [INFO] DFAST_QC result json was written to GCA_002492425.1_ASM249242v1_genomic.fna/dqc_result.json
[2023-06-28 10:23:05,955] [INFO] DFAST_QC completed!
[2023-06-28 10:23:05,955] [INFO] Total running time: 0h0m58s