[2023-06-19 01:46:19,362] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:46:19,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:46:19,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference
[2023-06-19 01:46:21,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:46:21,115] [INFO] Task started: Prodigal
[2023-06-19 01:46:21,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg8355ff11-675b-40a7-993d-f251f0ece026/GCA_018433175.1_SV1_genomic.fna.gz | prodigal -d GCA_018433175.1_SV1_genomic.fna/cds.fna -a GCA_018433175.1_SV1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:46:31,739] [INFO] Task succeeded: Prodigal
[2023-06-19 01:46:31,739] [INFO] Task started: HMMsearch
[2023-06-19 01:46:31,739] [INFO] Running command: hmmsearch --tblout GCA_018433175.1_SV1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/reference_markers.hmm GCA_018433175.1_SV1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:46:32,000] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:46:32,002] [INFO] Found 6/6 markers.
[2023-06-19 01:46:32,035] [INFO] Query marker FASTA was written to GCA_018433175.1_SV1_genomic.fna/markers.fasta
[2023-06-19 01:46:32,035] [INFO] Task started: Blastn
[2023-06-19 01:46:32,036] [INFO] Running command: blastn -query GCA_018433175.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/reference_markers.fasta -out GCA_018433175.1_SV1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:32,710] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:32,715] [INFO] Selected 32 target genomes.
[2023-06-19 01:46:32,716] [INFO] Target genome list was writen to GCA_018433175.1_SV1_genomic.fna/target_genomes.txt
[2023-06-19 01:46:32,718] [INFO] Task started: fastANI
[2023-06-19 01:46:32,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg8355ff11-675b-40a7-993d-f251f0ece026/GCA_018433175.1_SV1_genomic.fna.gz --refList GCA_018433175.1_SV1_genomic.fna/target_genomes.txt --output GCA_018433175.1_SV1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:46:53,356] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:53,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:46:53,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:46:53,365] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:46:53,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:46:53,366] [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
Proteiniphilum saccharofermentans	strain=M3/6	GCA_900095135.1	1642647	1642647	type	True	78.4375	97	617	95	below_threshold
Petrimonas mucosa	strain=ING2-E5A	GCA_900095795.1	1642646	1642646	type	True	78.1278	208	617	95	below_threshold
Proteiniphilum acetatigenes	strain=DSM 18083	GCA_000380985.1	294710	294710	type	True	77.9555	101	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:46:53,368] [INFO] DFAST Taxonomy check result was written to GCA_018433175.1_SV1_genomic.fna/tc_result.tsv
[2023-06-19 01:46:53,369] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:46:53,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:46:53,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/checkm_data
[2023-06-19 01:46:53,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:46:53,405] [INFO] Task started: CheckM
[2023-06-19 01:46:53,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433175.1_SV1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433175.1_SV1_genomic.fna/checkm_input GCA_018433175.1_SV1_genomic.fna/checkm_result
[2023-06-19 01:47:28,682] [INFO] Task succeeded: CheckM
[2023-06-19 01:47:28,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.97%
Contamintation: 4.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 01:47:28,717] [INFO] ===== Completeness check finished =====
[2023-06-19 01:47:28,718] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:47:28,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433175.1_SV1_genomic.fna/markers.fasta)
[2023-06-19 01:47:28,719] [INFO] Task started: Blastn
[2023-06-19 01:47:28,719] [INFO] Running command: blastn -query GCA_018433175.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12253e80-d04a-4dc3-ad66-ff3bcd1c9382/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433175.1_SV1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:47:29,545] [INFO] Task succeeded: Blastn
[2023-06-19 01:47:29,552] [INFO] Selected 10 target genomes.
[2023-06-19 01:47:29,552] [INFO] Target genome list was writen to GCA_018433175.1_SV1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:47:29,556] [INFO] Task started: fastANI
[2023-06-19 01:47:29,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg8355ff11-675b-40a7-993d-f251f0ece026/GCA_018433175.1_SV1_genomic.fna.gz --refList GCA_018433175.1_SV1_genomic.fna/target_genomes_gtdb.txt --output GCA_018433175.1_SV1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:47:35,670] [INFO] Task succeeded: fastANI
[2023-06-19 01:47:35,679] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:47:35,679] [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_001898165.1	s__Petrimonas sp001898165	98.7979	554	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	98.74	98.68	0.87	0.85	3	conclusive
GCA_002356435.2	s__Petrimonas sp002356435	82.9371	429	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	98.95	98.66	0.89	0.81	15	-
GCA_002316835.1	s__Petrimonas sp002316835	79.3296	275	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002069095.1	s__Petrimonas sp002069095	79.2804	210	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095795.1	s__Petrimonas mucosa	78.1278	208	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	99.51	99.34	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-19 01:47:35,681] [INFO] GTDB search result was written to GCA_018433175.1_SV1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:47:35,682] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:47:35,685] [INFO] DFAST_QC result json was written to GCA_018433175.1_SV1_genomic.fna/dqc_result.json
[2023-06-19 01:47:35,685] [INFO] DFAST_QC completed!
[2023-06-19 01:47:35,685] [INFO] Total running time: 0h1m16s