[2023-06-30 03:20:31,828] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:20:31,830] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:20:31,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg195c6513-cb7c-479d-855b-5f9b4a80d22b/dqc_reference
[2023-06-30 03:20:34,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:20:34,216] [INFO] Task started: Prodigal
[2023-06-30 03:20:34,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg28a5e004-2d91-4189-acd6-5124473dbac4/GCA_008933285.1_ASM893328v1_genomic.fna.gz | prodigal -d GCA_008933285.1_ASM893328v1_genomic.fna/cds.fna -a GCA_008933285.1_ASM893328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:20:38,786] [INFO] Task succeeded: Prodigal
[2023-06-30 03:20:38,786] [INFO] Task started: HMMsearch
[2023-06-30 03:20:38,787] [INFO] Running command: hmmsearch --tblout GCA_008933285.1_ASM893328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg195c6513-cb7c-479d-855b-5f9b4a80d22b/dqc_reference/reference_markers.hmm GCA_008933285.1_ASM893328v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:20:38,981] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:20:38,983] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg28a5e004-2d91-4189-acd6-5124473dbac4/GCA_008933285.1_ASM893328v1_genomic.fna.gz]
[2023-06-30 03:20:39,009] [INFO] Query marker FASTA was written to GCA_008933285.1_ASM893328v1_genomic.fna/markers.fasta
[2023-06-30 03:20:39,010] [INFO] Task started: Blastn
[2023-06-30 03:20:39,010] [INFO] Running command: blastn -query GCA_008933285.1_ASM893328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195c6513-cb7c-479d-855b-5f9b4a80d22b/dqc_reference/reference_markers.fasta -out GCA_008933285.1_ASM893328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:20:39,533] [INFO] Task succeeded: Blastn
[2023-06-30 03:20:39,537] [INFO] Selected 0 target genomes.
[2023-06-30 03:20:39,538] [INFO] Target genome list was writen to GCA_008933285.1_ASM893328v1_genomic.fna/target_genomes.txt
[2023-06-30 03:20:39,538] [ERROR] File is empty. [GCA_008933285.1_ASM893328v1_genomic.fna/target_genomes.txt]
[2023-06-30 03:20:39,538] [ERROR] Task failed. No target genome found.
[2023-06-30 03:20:39,539] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:20:39,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg195c6513-cb7c-479d-855b-5f9b4a80d22b/dqc_reference/checkm_data
[2023-06-30 03:20:39,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:20:39,571] [INFO] Task started: CheckM
[2023-06-30 03:20:39,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008933285.1_ASM893328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008933285.1_ASM893328v1_genomic.fna/checkm_input GCA_008933285.1_ASM893328v1_genomic.fna/checkm_result
[2023-06-30 03:21:03,202] [INFO] Task succeeded: CheckM
[2023-06-30 03:21:03,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:21:03,226] [INFO] ===== Completeness check finished =====
[2023-06-30 03:21:03,226] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:21:03,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008933285.1_ASM893328v1_genomic.fna/markers.fasta)
[2023-06-30 03:21:03,227] [INFO] Task started: Blastn
[2023-06-30 03:21:03,227] [INFO] Running command: blastn -query GCA_008933285.1_ASM893328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195c6513-cb7c-479d-855b-5f9b4a80d22b/dqc_reference/reference_markers_gtdb.fasta -out GCA_008933285.1_ASM893328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:21:03,891] [INFO] Task succeeded: Blastn
[2023-06-30 03:21:03,896] [INFO] Selected 11 target genomes.
[2023-06-30 03:21:03,896] [INFO] Target genome list was writen to GCA_008933285.1_ASM893328v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:21:03,914] [INFO] Task started: fastANI
[2023-06-30 03:21:03,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a5e004-2d91-4189-acd6-5124473dbac4/GCA_008933285.1_ASM893328v1_genomic.fna.gz --refList GCA_008933285.1_ASM893328v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008933285.1_ASM893328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:21:11,204] [INFO] Task succeeded: fastANI
[2023-06-30 03:21:11,218] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:21:11,218] [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_002009475.1	s__Brocadia caroliniensis	89.2484	305	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007618135.1	s__Brocadia sp007618135	87.8134	290	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017347445.1	s__Brocadia pituitae	83.8662	280	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000987375.1	s__Brocadia fulgida	81.3712	258	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	98.97	98.40	0.88	0.87	4	-
GCF_001753675.2	s__Brocadia sapporoensis	80.0207	204	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	97.53	96.30	0.92	0.89	8	-
GCA_015075005.1	s__Brocadia sp015075005	78.9473	179	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360945.1	s__Brocadia sp013360945	78.5022	174	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Brocadia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696655.1	s__Jettenia sp900696655	77.6777	51	379	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Brocadiaceae;g__Jettenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:21:11,221] [INFO] GTDB search result was written to GCA_008933285.1_ASM893328v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:21:11,222] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:21:11,225] [INFO] DFAST_QC result json was written to GCA_008933285.1_ASM893328v1_genomic.fna/dqc_result.json
[2023-06-30 03:21:11,226] [INFO] DFAST_QC completed!
[2023-06-30 03:21:11,226] [INFO] Total running time: 0h0m39s