[2023-06-17 01:08:20,012] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:08:20,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:08:20,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a2edccc-8b56-47a7-ad6a-d956de887672/dqc_reference
[2023-06-17 01:08:21,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:08:21,612] [INFO] Task started: Prodigal
[2023-06-17 01:08:21,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a3d121f-3051-4003-b0fc-6639c2d4ba47/GCA_013154145.1_ASM1315414v1_genomic.fna.gz | prodigal -d GCA_013154145.1_ASM1315414v1_genomic.fna/cds.fna -a GCA_013154145.1_ASM1315414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:08:24,343] [INFO] Task succeeded: Prodigal
[2023-06-17 01:08:24,344] [INFO] Task started: HMMsearch
[2023-06-17 01:08:24,344] [INFO] Running command: hmmsearch --tblout GCA_013154145.1_ASM1315414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a2edccc-8b56-47a7-ad6a-d956de887672/dqc_reference/reference_markers.hmm GCA_013154145.1_ASM1315414v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:08:24,508] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:08:24,509] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3a3d121f-3051-4003-b0fc-6639c2d4ba47/GCA_013154145.1_ASM1315414v1_genomic.fna.gz]
[2023-06-17 01:08:24,523] [INFO] Query marker FASTA was written to GCA_013154145.1_ASM1315414v1_genomic.fna/markers.fasta
[2023-06-17 01:08:24,523] [INFO] Task started: Blastn
[2023-06-17 01:08:24,523] [INFO] Running command: blastn -query GCA_013154145.1_ASM1315414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2edccc-8b56-47a7-ad6a-d956de887672/dqc_reference/reference_markers.fasta -out GCA_013154145.1_ASM1315414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:26,192] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:26,195] [INFO] Selected 0 target genomes.
[2023-06-17 01:08:26,195] [INFO] Target genome list was writen to GCA_013154145.1_ASM1315414v1_genomic.fna/target_genomes.txt
[2023-06-17 01:08:26,195] [ERROR] File is empty. [GCA_013154145.1_ASM1315414v1_genomic.fna/target_genomes.txt]
[2023-06-17 01:08:26,196] [ERROR] Task failed. No target genome found.
[2023-06-17 01:08:26,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:08:26,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a2edccc-8b56-47a7-ad6a-d956de887672/dqc_reference/checkm_data
[2023-06-17 01:08:26,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:08:26,207] [INFO] Task started: CheckM
[2023-06-17 01:08:26,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013154145.1_ASM1315414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013154145.1_ASM1315414v1_genomic.fna/checkm_input GCA_013154145.1_ASM1315414v1_genomic.fna/checkm_result
[2023-06-17 01:08:45,012] [INFO] Task succeeded: CheckM
[2023-06-17 01:08:45,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 01:08:45,034] [INFO] ===== Completeness check finished =====
[2023-06-17 01:08:45,035] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:08:45,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013154145.1_ASM1315414v1_genomic.fna/markers.fasta)
[2023-06-17 01:08:45,036] [INFO] Task started: Blastn
[2023-06-17 01:08:45,036] [INFO] Running command: blastn -query GCA_013154145.1_ASM1315414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2edccc-8b56-47a7-ad6a-d956de887672/dqc_reference/reference_markers_gtdb.fasta -out GCA_013154145.1_ASM1315414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:45,496] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:45,500] [INFO] Selected 1 target genomes.
[2023-06-17 01:08:45,500] [INFO] Target genome list was writen to GCA_013154145.1_ASM1315414v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:08:45,502] [INFO] Task started: fastANI
[2023-06-17 01:08:45,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3d121f-3051-4003-b0fc-6639c2d4ba47/GCA_013154145.1_ASM1315414v1_genomic.fna.gz --refList GCA_013154145.1_ASM1315414v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013154145.1_ASM1315414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:08:45,686] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:45,691] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:08:45,691] [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_013154145.1	s__JAADDC01 sp013154145	100.0	138	141	d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o__JAADDC01;f__JAADDC01;g__JAADDC01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-17 01:08:45,694] [INFO] GTDB search result was written to GCA_013154145.1_ASM1315414v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:08:45,694] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:08:45,697] [INFO] DFAST_QC result json was written to GCA_013154145.1_ASM1315414v1_genomic.fna/dqc_result.json
[2023-06-17 01:08:45,697] [INFO] DFAST_QC completed!
[2023-06-17 01:08:45,698] [INFO] Total running time: 0h0m26s