[2023-06-29 20:13:49,175] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:13:49,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:13:49,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference
[2023-06-29 20:13:50,413] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:13:50,414] [INFO] Task started: Prodigal
[2023-06-29 20:13:50,414] [INFO] Running command: gunzip -c /var/lib/cwl/stgf07dcdc9-4eed-430b-a937-8832f457adfe/GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:13:54,428] [INFO] Task succeeded: Prodigal
[2023-06-29 20:13:54,429] [INFO] Task started: HMMsearch
[2023-06-29 20:13:54,429] [INFO] Running command: hmmsearch --tblout GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/reference_markers.hmm GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:13:54,619] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:13:54,620] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf07dcdc9-4eed-430b-a937-8832f457adfe/GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 20:13:54,649] [INFO] Query marker FASTA was written to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 20:13:54,649] [INFO] Task started: Blastn
[2023-06-29 20:13:54,649] [INFO] Running command: blastn -query GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/reference_markers.fasta -out GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:13:55,256] [INFO] Task succeeded: Blastn
[2023-06-29 20:13:55,259] [INFO] Selected 19 target genomes.
[2023-06-29 20:13:55,259] [INFO] Target genome list was writen to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 20:13:55,261] [INFO] Task started: fastANI
[2023-06-29 20:13:55,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgf07dcdc9-4eed-430b-a937-8832f457adfe/GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:05,565] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:05,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:05,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:05,570] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:05,571] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:14:05,571] [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
Catonella massiliensis	strain=Marseille-Q4567	GCA_016651435.1	2799636	2799636	type	True	94.6939	519	612	95	below_threshold
Catonella morbi	strain=ATCC 51271	GCA_000160035.2	43997	43997	type	True	80.683	374	612	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:14:05,573] [INFO] DFAST Taxonomy check result was written to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 20:14:05,573] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:05,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:05,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/checkm_data
[2023-06-29 20:14:05,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:05,601] [INFO] Task started: CheckM
[2023-06-29 20:14:05,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 20:14:24,575] [INFO] Task succeeded: CheckM
[2023-06-29 20:14:24,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:14:24,594] [INFO] ===== Completeness check finished =====
[2023-06-29 20:14:24,594] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:14:24,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 20:14:24,595] [INFO] Task started: Blastn
[2023-06-29 20:14:24,595] [INFO] Running command: blastn -query GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ece8f0f-d8bf-49bb-9988-bc0af7c2afab/dqc_reference/reference_markers_gtdb.fasta -out GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:25,577] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:25,580] [INFO] Selected 18 target genomes.
[2023-06-29 20:14:25,580] [INFO] Target genome list was writen to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:14:25,586] [INFO] Task started: fastANI
[2023-06-29 20:14:25,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgf07dcdc9-4eed-430b-a937-8832f457adfe/GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:14:33,724] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:33,727] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:14:33,728] [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
GCF_016651435.1	s__Catonella massiliensis	94.6939	519	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	95.56	95.38	0.94	0.93	3	-
GCF_000160035.2	s__Catonella morbi	80.6734	375	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:14:33,729] [INFO] GTDB search result was written to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 20:14:33,730] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:14:33,732] [INFO] DFAST_QC result json was written to GCA_937893255.1_SRR1952431_bin.73_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 20:14:33,732] [INFO] DFAST_QC completed!
[2023-06-29 20:14:33,732] [INFO] Total running time: 0h0m45s