[2023-06-13 22:21:32,314] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:21:32,317] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:21:32,317] [INFO] DQC Reference Directory: /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference
[2023-06-13 22:21:34,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:21:34,098] [INFO] Task started: Prodigal
[2023-06-13 22:21:34,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b13656f-6c87-4eee-ae6f-d1c6d02a2727/GCA_022708545.1_ASM2270854v1_genomic.fna.gz | prodigal -d GCA_022708545.1_ASM2270854v1_genomic.fna/cds.fna -a GCA_022708545.1_ASM2270854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:21:44,481] [INFO] Task succeeded: Prodigal
[2023-06-13 22:21:44,482] [INFO] Task started: HMMsearch
[2023-06-13 22:21:44,482] [INFO] Running command: hmmsearch --tblout GCA_022708545.1_ASM2270854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/reference_markers.hmm GCA_022708545.1_ASM2270854v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:21:44,728] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:21:44,729] [INFO] Found 6/6 markers.
[2023-06-13 22:21:44,755] [INFO] Query marker FASTA was written to GCA_022708545.1_ASM2270854v1_genomic.fna/markers.fasta
[2023-06-13 22:21:44,755] [INFO] Task started: Blastn
[2023-06-13 22:21:44,755] [INFO] Running command: blastn -query GCA_022708545.1_ASM2270854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/reference_markers.fasta -out GCA_022708545.1_ASM2270854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:21:45,330] [INFO] Task succeeded: Blastn
[2023-06-13 22:21:45,334] [INFO] Selected 24 target genomes.
[2023-06-13 22:21:45,335] [INFO] Target genome list was writen to GCA_022708545.1_ASM2270854v1_genomic.fna/target_genomes.txt
[2023-06-13 22:21:45,336] [INFO] Task started: fastANI
[2023-06-13 22:21:45,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b13656f-6c87-4eee-ae6f-d1c6d02a2727/GCA_022708545.1_ASM2270854v1_genomic.fna.gz --refList GCA_022708545.1_ASM2270854v1_genomic.fna/target_genomes.txt --output GCA_022708545.1_ASM2270854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:22:01,890] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:01,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:22:01,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:22:01,897] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 22:22:01,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 22:22:01,897] [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
Seramator thermalis	strain=SYSU GA16112	GCA_004138125.1	2496270	2496270	type	True	96.6949	631	717	95	conclusive
Petrimonas mucosa	strain=ING2-E5A	GCA_900095795.1	1642646	1642646	type	True	76.6595	64	717	95	below_threshold
Proteiniphilum saccharofermentans	strain=M3/6	GCA_900095135.1	1642647	1642647	type	True	76.2951	67	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:22:01,899] [INFO] DFAST Taxonomy check result was written to GCA_022708545.1_ASM2270854v1_genomic.fna/tc_result.tsv
[2023-06-13 22:22:01,900] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:22:01,900] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:22:01,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/checkm_data
[2023-06-13 22:22:01,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:22:01,935] [INFO] Task started: CheckM
[2023-06-13 22:22:01,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708545.1_ASM2270854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708545.1_ASM2270854v1_genomic.fna/checkm_input GCA_022708545.1_ASM2270854v1_genomic.fna/checkm_result
[2023-06-13 22:22:35,264] [INFO] Task succeeded: CheckM
[2023-06-13 22:22:35,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 8.68%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-13 22:22:35,300] [INFO] ===== Completeness check finished =====
[2023-06-13 22:22:35,300] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:22:35,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708545.1_ASM2270854v1_genomic.fna/markers.fasta)
[2023-06-13 22:22:35,302] [INFO] Task started: Blastn
[2023-06-13 22:22:35,302] [INFO] Running command: blastn -query GCA_022708545.1_ASM2270854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8aef1f1-5916-4349-b629-4a017e63e07a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708545.1_ASM2270854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:22:36,080] [INFO] Task succeeded: Blastn
[2023-06-13 22:22:36,086] [INFO] Selected 30 target genomes.
[2023-06-13 22:22:36,086] [INFO] Target genome list was writen to GCA_022708545.1_ASM2270854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:22:36,093] [INFO] Task started: fastANI
[2023-06-13 22:22:36,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b13656f-6c87-4eee-ae6f-d1c6d02a2727/GCA_022708545.1_ASM2270854v1_genomic.fna.gz --refList GCA_022708545.1_ASM2270854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708545.1_ASM2270854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:22:51,158] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:51,165] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 22:22:51,165] [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_002849245.1	s__UBA4179 sp002849245	95.1682	624	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__UBA4179	95.0	95.42	95.13	0.87	0.84	8	conclusive
GCA_002381125.1	s__UBA4179 sp002381125	79.3383	104	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__UBA4179	95.0	98.91	96.44	0.90	0.79	8	-
GCA_012798745.1	s__UBA4179 sp012798745	76.8374	56	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__UBA4179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316835.1	s__Petrimonas sp002316835	76.6652	64	717	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	76.6573	65	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	99.51	99.34	0.92	0.89	3	-
GCA_002383605.1	s__Proteiniphilum sp002383605	76.6174	73	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.07	99.07	0.78	0.78	2	-
GCA_001768325.1	s__Proteiniphilum sp001768325	76.5016	77	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.21	95.58	0.95	0.81	7	-
GCF_900095135.1	s__Proteiniphilum saccharofermentans	76.3098	68	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	96.87	96.82	0.85	0.85	3	-
GCA_002069095.1	s__Petrimonas sp002069095	76.1011	55	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:22:51,167] [INFO] GTDB search result was written to GCA_022708545.1_ASM2270854v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:22:51,167] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:22:51,169] [INFO] DFAST_QC result json was written to GCA_022708545.1_ASM2270854v1_genomic.fna/dqc_result.json
[2023-06-13 22:22:51,170] [INFO] DFAST_QC completed!
[2023-06-13 22:22:51,170] [INFO] Total running time: 0h1m19s