[2023-06-28 00:49:20,982] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:49:20,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:49:20,984] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf0c641-70b4-4f39-8bfb-3018b904fb76/dqc_reference
[2023-06-28 00:49:22,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:49:22,270] [INFO] Task started: Prodigal
[2023-06-28 00:49:22,270] [INFO] Running command: gunzip -c /var/lib/cwl/stgae005dc4-73c1-49a3-88e3-5c1c93d798ba/GCA_026396455.1_ASM2639645v1_genomic.fna.gz | prodigal -d GCA_026396455.1_ASM2639645v1_genomic.fna/cds.fna -a GCA_026396455.1_ASM2639645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:49:24,118] [INFO] Task succeeded: Prodigal
[2023-06-28 00:49:24,118] [INFO] Task started: HMMsearch
[2023-06-28 00:49:24,118] [INFO] Running command: hmmsearch --tblout GCA_026396455.1_ASM2639645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf0c641-70b4-4f39-8bfb-3018b904fb76/dqc_reference/reference_markers.hmm GCA_026396455.1_ASM2639645v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:49:24,301] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:49:24,303] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgae005dc4-73c1-49a3-88e3-5c1c93d798ba/GCA_026396455.1_ASM2639645v1_genomic.fna.gz]
[2023-06-28 00:49:24,318] [INFO] Query marker FASTA was written to GCA_026396455.1_ASM2639645v1_genomic.fna/markers.fasta
[2023-06-28 00:49:24,319] [INFO] Task started: Blastn
[2023-06-28 00:49:24,319] [INFO] Running command: blastn -query GCA_026396455.1_ASM2639645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf0c641-70b4-4f39-8bfb-3018b904fb76/dqc_reference/reference_markers.fasta -out GCA_026396455.1_ASM2639645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:49:25,849] [INFO] Task succeeded: Blastn
[2023-06-28 00:49:25,854] [INFO] Selected 0 target genomes.
[2023-06-28 00:49:25,854] [INFO] Target genome list was writen to GCA_026396455.1_ASM2639645v1_genomic.fna/target_genomes.txt
[2023-06-28 00:49:25,855] [ERROR] File is empty. [GCA_026396455.1_ASM2639645v1_genomic.fna/target_genomes.txt]
[2023-06-28 00:49:25,855] [ERROR] Task failed. No target genome found.
[2023-06-28 00:49:25,855] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:49:25,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf0c641-70b4-4f39-8bfb-3018b904fb76/dqc_reference/checkm_data
[2023-06-28 00:49:25,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:49:25,903] [INFO] Task started: CheckM
[2023-06-28 00:49:25,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026396455.1_ASM2639645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026396455.1_ASM2639645v1_genomic.fna/checkm_input GCA_026396455.1_ASM2639645v1_genomic.fna/checkm_result
[2023-06-28 00:49:42,426] [INFO] Task succeeded: CheckM
[2023-06-28 00:49:42,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 00:49:42,450] [INFO] ===== Completeness check finished =====
[2023-06-28 00:49:42,451] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:49:42,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026396455.1_ASM2639645v1_genomic.fna/markers.fasta)
[2023-06-28 00:49:42,451] [INFO] Task started: Blastn
[2023-06-28 00:49:42,452] [INFO] Running command: blastn -query GCA_026396455.1_ASM2639645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf0c641-70b4-4f39-8bfb-3018b904fb76/dqc_reference/reference_markers_gtdb.fasta -out GCA_026396455.1_ASM2639645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:49:43,029] [INFO] Task succeeded: Blastn
[2023-06-28 00:49:43,034] [INFO] Selected 3 target genomes.
[2023-06-28 00:49:43,034] [INFO] Target genome list was writen to GCA_026396455.1_ASM2639645v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:49:43,056] [INFO] Task started: fastANI
[2023-06-28 00:49:43,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgae005dc4-73c1-49a3-88e3-5c1c93d798ba/GCA_026396455.1_ASM2639645v1_genomic.fna.gz --refList GCA_026396455.1_ASM2639645v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026396455.1_ASM2639645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:49:43,882] [INFO] Task succeeded: fastANI
[2023-06-28 00:49:43,886] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:49:43,886] [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_013426015.1	s__Fermentimicrarchaeum limneticum	78.9617	112	230	d__Archaea;p__Micrarchaeota;c__Micrarchaeia;o__DTNL01;f__DTGH01;g__Fermentimicrarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013425405.1	s__Fermentimicrarchaeum sp013425405	78.8171	113	230	d__Archaea;p__Micrarchaeota;c__Micrarchaeia;o__DTNL01;f__DTGH01;g__Fermentimicrarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:49:43,888] [INFO] GTDB search result was written to GCA_026396455.1_ASM2639645v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:49:43,889] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:49:43,891] [INFO] DFAST_QC result json was written to GCA_026396455.1_ASM2639645v1_genomic.fna/dqc_result.json
[2023-06-28 00:49:43,892] [INFO] DFAST_QC completed!
[2023-06-28 00:49:43,892] [INFO] Total running time: 0h0m23s