[2023-06-29 15:23:25,386] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:23:25,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:23:25,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference
[2023-06-29 15:23:26,585] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:23:26,586] [INFO] Task started: Prodigal
[2023-06-29 15:23:26,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f5b643f-cf1c-4a47-a50d-856971b6e4d9/GCA_021737265.1_ASM2173726v1_genomic.fna.gz | prodigal -d GCA_021737265.1_ASM2173726v1_genomic.fna/cds.fna -a GCA_021737265.1_ASM2173726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:23:34,046] [INFO] Task succeeded: Prodigal
[2023-06-29 15:23:34,046] [INFO] Task started: HMMsearch
[2023-06-29 15:23:34,046] [INFO] Running command: hmmsearch --tblout GCA_021737265.1_ASM2173726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/reference_markers.hmm GCA_021737265.1_ASM2173726v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:23:34,331] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:23:34,332] [INFO] Found 6/6 markers.
[2023-06-29 15:23:34,365] [INFO] Query marker FASTA was written to GCA_021737265.1_ASM2173726v1_genomic.fna/markers.fasta
[2023-06-29 15:23:34,365] [INFO] Task started: Blastn
[2023-06-29 15:23:34,366] [INFO] Running command: blastn -query GCA_021737265.1_ASM2173726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/reference_markers.fasta -out GCA_021737265.1_ASM2173726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:23:34,955] [INFO] Task succeeded: Blastn
[2023-06-29 15:23:34,959] [INFO] Selected 24 target genomes.
[2023-06-29 15:23:34,960] [INFO] Target genome list was writen to GCA_021737265.1_ASM2173726v1_genomic.fna/target_genomes.txt
[2023-06-29 15:23:34,966] [INFO] Task started: fastANI
[2023-06-29 15:23:34,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f5b643f-cf1c-4a47-a50d-856971b6e4d9/GCA_021737265.1_ASM2173726v1_genomic.fna.gz --refList GCA_021737265.1_ASM2173726v1_genomic.fna/target_genomes.txt --output GCA_021737265.1_ASM2173726v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:23:49,563] [INFO] Task succeeded: fastANI
[2023-06-29 15:23:49,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:23:49,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:23:49,568] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:23:49,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:23:49,569] [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
Desulfocapsa sulfexigens	strain=DSM 10523	GCA_000341395.1	65555	65555	type	True	77.5842	202	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:23:49,571] [INFO] DFAST Taxonomy check result was written to GCA_021737265.1_ASM2173726v1_genomic.fna/tc_result.tsv
[2023-06-29 15:23:49,572] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:23:49,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:23:49,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/checkm_data
[2023-06-29 15:23:49,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:23:49,608] [INFO] Task started: CheckM
[2023-06-29 15:23:49,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021737265.1_ASM2173726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021737265.1_ASM2173726v1_genomic.fna/checkm_input GCA_021737265.1_ASM2173726v1_genomic.fna/checkm_result
[2023-06-29 15:24:18,683] [INFO] Task succeeded: CheckM
[2023-06-29 15:24:18,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:24:18,711] [INFO] ===== Completeness check finished =====
[2023-06-29 15:24:18,711] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:24:18,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021737265.1_ASM2173726v1_genomic.fna/markers.fasta)
[2023-06-29 15:24:18,712] [INFO] Task started: Blastn
[2023-06-29 15:24:18,712] [INFO] Running command: blastn -query GCA_021737265.1_ASM2173726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ddd95e3-179c-41c1-a141-ce4f005cb547/dqc_reference/reference_markers_gtdb.fasta -out GCA_021737265.1_ASM2173726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:24:19,497] [INFO] Task succeeded: Blastn
[2023-06-29 15:24:19,503] [INFO] Selected 26 target genomes.
[2023-06-29 15:24:19,503] [INFO] Target genome list was writen to GCA_021737265.1_ASM2173726v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:24:19,548] [INFO] Task started: fastANI
[2023-06-29 15:24:19,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f5b643f-cf1c-4a47-a50d-856971b6e4d9/GCA_021737265.1_ASM2173726v1_genomic.fna.gz --refList GCA_021737265.1_ASM2173726v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021737265.1_ASM2173726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:24:34,499] [INFO] Task succeeded: fastANI
[2023-06-29 15:24:34,510] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:24:34,511] [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_015662865.1	s__Desulfocapsa sulfexigens_B	77.963	186	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341395.1	s__Desulfocapsa sulfexigens	77.5842	202	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661935.1	s__Desulfocapsa sulfexigens_A	77.4245	124	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817385.1	s__Desulfocapsa sp018817385	77.4161	218	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	99.94	99.94	0.97	0.97	2	-
GCA_018820855.1	s__Desulfocapsa sp018820855	77.3212	224	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	99.68	99.21	0.96	0.95	4	-
GCA_016765495.1	s__Desulfocapsa sp016765495	77.3117	175	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891045.1	s__UBA2270 sp903891045	76.7787	50	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.69	99.69	0.87	0.87	2	-
GCA_019163335.1	s__UBA2270 sp019163335	76.6705	60	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424635.1	s__UBA2270 sp002424635	76.5926	55	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327225.1	s__UBA2270 sp002327225	76.4897	55	946	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:24:34,513] [INFO] GTDB search result was written to GCA_021737265.1_ASM2173726v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:24:34,514] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:24:34,517] [INFO] DFAST_QC result json was written to GCA_021737265.1_ASM2173726v1_genomic.fna/dqc_result.json
[2023-06-29 15:24:34,517] [INFO] DFAST_QC completed!
[2023-06-29 15:24:34,517] [INFO] Total running time: 0h1m9s