[2023-06-17 14:48:21,333] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:21,335] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:21,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg4284a4c2-a84e-428c-b1da-073aa030a754/dqc_reference
[2023-06-17 14:48:22,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:48:22,558] [INFO] Task started: Prodigal
[2023-06-17 14:48:22,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg736516be-45e7-445f-96bd-1bb436c99fd2/GCA_003019345.1_ASM301934v1_genomic.fna.gz | prodigal -d GCA_003019345.1_ASM301934v1_genomic.fna/cds.fna -a GCA_003019345.1_ASM301934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:48:27,626] [INFO] Task succeeded: Prodigal
[2023-06-17 14:48:27,627] [INFO] Task started: HMMsearch
[2023-06-17 14:48:27,627] [INFO] Running command: hmmsearch --tblout GCA_003019345.1_ASM301934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4284a4c2-a84e-428c-b1da-073aa030a754/dqc_reference/reference_markers.hmm GCA_003019345.1_ASM301934v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:48:27,774] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:48:27,776] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg736516be-45e7-445f-96bd-1bb436c99fd2/GCA_003019345.1_ASM301934v1_genomic.fna.gz]
[2023-06-17 14:48:27,796] [INFO] Query marker FASTA was written to GCA_003019345.1_ASM301934v1_genomic.fna/markers.fasta
[2023-06-17 14:48:27,796] [INFO] Task started: Blastn
[2023-06-17 14:48:27,797] [INFO] Running command: blastn -query GCA_003019345.1_ASM301934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4284a4c2-a84e-428c-b1da-073aa030a754/dqc_reference/reference_markers.fasta -out GCA_003019345.1_ASM301934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:48:28,254] [INFO] Task succeeded: Blastn
[2023-06-17 14:48:28,257] [INFO] Selected 0 target genomes.
[2023-06-17 14:48:28,258] [INFO] Target genome list was writen to GCA_003019345.1_ASM301934v1_genomic.fna/target_genomes.txt
[2023-06-17 14:48:28,258] [ERROR] File is empty. [GCA_003019345.1_ASM301934v1_genomic.fna/target_genomes.txt]
[2023-06-17 14:48:28,258] [ERROR] Task failed. No target genome found.
[2023-06-17 14:48:28,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:48:28,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4284a4c2-a84e-428c-b1da-073aa030a754/dqc_reference/checkm_data
[2023-06-17 14:48:28,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:48:28,277] [INFO] Task started: CheckM
[2023-06-17 14:48:28,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003019345.1_ASM301934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003019345.1_ASM301934v1_genomic.fna/checkm_input GCA_003019345.1_ASM301934v1_genomic.fna/checkm_result
[2023-06-17 14:48:49,528] [INFO] Task succeeded: CheckM
[2023-06-17 14:48:49,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.89%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:48:49,551] [INFO] ===== Completeness check finished =====
[2023-06-17 14:48:49,552] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:48:49,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003019345.1_ASM301934v1_genomic.fna/markers.fasta)
[2023-06-17 14:48:49,552] [INFO] Task started: Blastn
[2023-06-17 14:48:49,553] [INFO] Running command: blastn -query GCA_003019345.1_ASM301934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4284a4c2-a84e-428c-b1da-073aa030a754/dqc_reference/reference_markers_gtdb.fasta -out GCA_003019345.1_ASM301934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:48:49,960] [INFO] Task succeeded: Blastn
[2023-06-17 14:48:49,965] [INFO] Selected 2 target genomes.
[2023-06-17 14:48:49,965] [INFO] Target genome list was writen to GCA_003019345.1_ASM301934v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:48:49,970] [INFO] Task started: fastANI
[2023-06-17 14:48:49,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg736516be-45e7-445f-96bd-1bb436c99fd2/GCA_003019345.1_ASM301934v1_genomic.fna.gz --refList GCA_003019345.1_ASM301934v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003019345.1_ASM301934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:48:50,857] [INFO] Task succeeded: fastANI
[2023-06-17 14:48:50,864] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:48:50,864] [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_003019535.1	s__ECH-B-1 sp003019535	97.8298	307	336	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Marsarchaeales;f__Marsarchaeaceae;g__ECH-B-1	95.0	98.82	97.83	0.92	0.84	6	conclusive
GCA_902812505.1	s__ECH-B-1 sp902812505	94.328	170	336	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Marsarchaeales;f__Marsarchaeaceae;g__ECH-B-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:48:50,867] [INFO] GTDB search result was written to GCA_003019345.1_ASM301934v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:48:50,867] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:48:50,870] [INFO] DFAST_QC result json was written to GCA_003019345.1_ASM301934v1_genomic.fna/dqc_result.json
[2023-06-17 14:48:50,870] [INFO] DFAST_QC completed!
[2023-06-17 14:48:50,870] [INFO] Total running time: 0h0m30s