[2023-06-05 07:09:45,375] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:45,386] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:45,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgef032fba-f43e-4b6d-a490-d265956251cc/dqc_reference
[2023-06-05 07:09:47,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:47,004] [INFO] Task started: Prodigal
[2023-06-05 07:09:47,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bff3382-91c2-4243-aa1a-70938bf61cd0/GCA_004376705.1_ASM437670v1_genomic.fna.gz | prodigal -d GCA_004376705.1_ASM437670v1_genomic.fna/cds.fna -a GCA_004376705.1_ASM437670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:50,796] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:50,796] [INFO] Task started: HMMsearch
[2023-06-05 07:09:50,797] [INFO] Running command: hmmsearch --tblout GCA_004376705.1_ASM437670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef032fba-f43e-4b6d-a490-d265956251cc/dqc_reference/reference_markers.hmm GCA_004376705.1_ASM437670v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:51,055] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:51,056] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4bff3382-91c2-4243-aa1a-70938bf61cd0/GCA_004376705.1_ASM437670v1_genomic.fna.gz]
[2023-06-05 07:09:51,083] [INFO] Query marker FASTA was written to GCA_004376705.1_ASM437670v1_genomic.fna/markers.fasta
[2023-06-05 07:09:51,083] [INFO] Task started: Blastn
[2023-06-05 07:09:51,083] [INFO] Running command: blastn -query GCA_004376705.1_ASM437670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef032fba-f43e-4b6d-a490-d265956251cc/dqc_reference/reference_markers.fasta -out GCA_004376705.1_ASM437670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:51,593] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:51,596] [INFO] Selected 0 target genomes.
[2023-06-05 07:09:51,597] [INFO] Target genome list was writen to GCA_004376705.1_ASM437670v1_genomic.fna/target_genomes.txt
[2023-06-05 07:09:51,597] [ERROR] File is empty. [GCA_004376705.1_ASM437670v1_genomic.fna/target_genomes.txt]
[2023-06-05 07:09:51,597] [ERROR] Task failed. No target genome found.
[2023-06-05 07:09:51,597] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:09:51,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef032fba-f43e-4b6d-a490-d265956251cc/dqc_reference/checkm_data
[2023-06-05 07:09:51,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:09:51,630] [INFO] Task started: CheckM
[2023-06-05 07:09:51,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004376705.1_ASM437670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004376705.1_ASM437670v1_genomic.fna/checkm_input GCA_004376705.1_ASM437670v1_genomic.fna/checkm_result
[2023-06-05 07:10:12,399] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:12,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 1.14%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:10:12,421] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:12,421] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:12,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004376705.1_ASM437670v1_genomic.fna/markers.fasta)
[2023-06-05 07:10:12,422] [INFO] Task started: Blastn
[2023-06-05 07:10:12,422] [INFO] Running command: blastn -query GCA_004376705.1_ASM437670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef032fba-f43e-4b6d-a490-d265956251cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_004376705.1_ASM437670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:12,934] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:12,939] [INFO] Selected 7 target genomes.
[2023-06-05 07:10:12,939] [INFO] Target genome list was writen to GCA_004376705.1_ASM437670v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:13,039] [INFO] Task started: fastANI
[2023-06-05 07:10:13,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bff3382-91c2-4243-aa1a-70938bf61cd0/GCA_004376705.1_ASM437670v1_genomic.fna.gz --refList GCA_004376705.1_ASM437670v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004376705.1_ASM437670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:10:18,069] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:18,082] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:10:18,082] [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_005223125.1	s__Loki-b32 sp005223125	96.0175	608	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	97.09	96.02	0.70	0.58	3	conclusive
GCA_013375485.1	s__Loki-b32 sp013375485	83.9317	517	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019058245.1	s__Loki-b32 sp019058245	79.323	317	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019057865.1	s__Loki-b32 sp019057865	77.5047	234	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	96.46	95.72	0.89	0.80	7	-
GCA_016839585.1	s__Loki-b32 sp016839585	77.1513	185	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016839705.1	s__Loki-b32 sp016839705	76.6865	143	733	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:10:18,084] [INFO] GTDB search result was written to GCA_004376705.1_ASM437670v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:10:18,085] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:10:18,087] [INFO] DFAST_QC result json was written to GCA_004376705.1_ASM437670v1_genomic.fna/dqc_result.json
[2023-06-05 07:10:18,087] [INFO] DFAST_QC completed!
[2023-06-05 07:10:18,087] [INFO] Total running time: 0h0m33s