[2023-06-29 13:46:56,028] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:46:56,030] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:46:56,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference
[2023-06-29 13:46:57,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:46:57,271] [INFO] Task started: Prodigal
[2023-06-29 13:46:57,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg51350147-2336-4457-aa7b-aef367b70ebd/GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:47:02,095] [INFO] Task succeeded: Prodigal
[2023-06-29 13:47:02,095] [INFO] Task started: HMMsearch
[2023-06-29 13:47:02,095] [INFO] Running command: hmmsearch --tblout GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/reference_markers.hmm GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:47:02,335] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:47:02,337] [INFO] Found 6/6 markers.
[2023-06-29 13:47:02,365] [INFO] Query marker FASTA was written to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:47:02,366] [INFO] Task started: Blastn
[2023-06-29 13:47:02,366] [INFO] Running command: blastn -query GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/reference_markers.fasta -out GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:47:02,939] [INFO] Task succeeded: Blastn
[2023-06-29 13:47:02,944] [INFO] Selected 14 target genomes.
[2023-06-29 13:47:02,944] [INFO] Target genome list was writen to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:47:02,946] [INFO] Task started: fastANI
[2023-06-29 13:47:02,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg51350147-2336-4457-aa7b-aef367b70ebd/GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:47:09,164] [INFO] Task succeeded: fastANI
[2023-06-29 13:47:09,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:47:09,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:47:09,167] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:47:09,167] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:47:09,167] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-29 13:47:09,169] [INFO] DFAST Taxonomy check result was written to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:47:09,170] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:47:09,170] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:47:09,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/checkm_data
[2023-06-29 13:47:09,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:47:09,204] [INFO] Task started: CheckM
[2023-06-29 13:47:09,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:47:30,673] [INFO] Task succeeded: CheckM
[2023-06-29 13:47:30,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 13:47:30,696] [INFO] ===== Completeness check finished =====
[2023-06-29 13:47:30,697] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:47:30,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:47:30,698] [INFO] Task started: Blastn
[2023-06-29 13:47:30,698] [INFO] Running command: blastn -query GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf52b3316-a805-4fba-87c4-eb7aa4c2efb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:47:31,462] [INFO] Task succeeded: Blastn
[2023-06-29 13:47:31,469] [INFO] Selected 21 target genomes.
[2023-06-29 13:47:31,469] [INFO] Target genome list was writen to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:47:31,518] [INFO] Task started: fastANI
[2023-06-29 13:47:31,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg51350147-2336-4457-aa7b-aef367b70ebd/GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:47:38,145] [INFO] Task succeeded: fastANI
[2023-06-29 13:47:38,148] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:47:38,149] [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_002428055.1	s__UBA6016 sp002428055	77.9509	171	708	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__UBA6016;g__UBA6016	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:47:38,151] [INFO] GTDB search result was written to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:47:38,152] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:47:38,155] [INFO] DFAST_QC result json was written to GCA_937973585.1_SRR6231178_bin.58_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:47:38,156] [INFO] DFAST_QC completed!
[2023-06-29 13:47:38,156] [INFO] Total running time: 0h0m42s