[2023-06-13 00:45:01,357] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:01,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:01,361] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference
[2023-06-13 00:45:02,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:02,638] [INFO] Task started: Prodigal
[2023-06-13 00:45:02,638] [INFO] Running command: gunzip -c /var/lib/cwl/stga5351910-7975-45d7-897e-2a3d78ec2df5/GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:08,858] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:08,859] [INFO] Task started: HMMsearch
[2023-06-13 00:45:08,859] [INFO] Running command: hmmsearch --tblout GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/reference_markers.hmm GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:09,157] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:09,159] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga5351910-7975-45d7-897e-2a3d78ec2df5/GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 00:45:09,191] [INFO] Query marker FASTA was written to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 00:45:09,191] [INFO] Task started: Blastn
[2023-06-13 00:45:09,191] [INFO] Running command: blastn -query GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/reference_markers.fasta -out GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:09,794] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:09,797] [INFO] Selected 7 target genomes.
[2023-06-13 00:45:09,798] [INFO] Target genome list was writen to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 00:45:09,801] [INFO] Task started: fastANI
[2023-06-13 00:45:09,801] [INFO] Running command: fastANI --query /var/lib/cwl/stga5351910-7975-45d7-897e-2a3d78ec2df5/GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:15,334] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:15,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:15,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:15,339] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:15,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:45:15,339] [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
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	78.2621	229	673	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	76.5299	60	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:45:15,341] [INFO] DFAST Taxonomy check result was written to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 00:45:15,342] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:15,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:15,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/checkm_data
[2023-06-13 00:45:15,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:15,376] [INFO] Task started: CheckM
[2023-06-13 00:45:15,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 00:45:40,907] [INFO] Task succeeded: CheckM
[2023-06-13 00:45:40,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:45:40,926] [INFO] ===== Completeness check finished =====
[2023-06-13 00:45:40,927] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:45:40,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 00:45:40,927] [INFO] Task started: Blastn
[2023-06-13 00:45:40,928] [INFO] Running command: blastn -query GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf525cb1-b143-4250-a12c-512192fab967/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:41,708] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:41,712] [INFO] Selected 25 target genomes.
[2023-06-13 00:45:41,712] [INFO] Target genome list was writen to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:45:41,741] [INFO] Task started: fastANI
[2023-06-13 00:45:41,741] [INFO] Running command: fastANI --query /var/lib/cwl/stga5351910-7975-45d7-897e-2a3d78ec2df5/GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:45:52,628] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:52,632] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:45:52,632] [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_900186535.1	s__Anaerotruncus massiliensis_A	78.2621	229	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.01	98.01	0.87	0.87	2	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	76.5299	60	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
--------------------------------------------------------------------------------
[2023-06-13 00:45:52,634] [INFO] GTDB search result was written to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 00:45:52,635] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:45:52,637] [INFO] DFAST_QC result json was written to GCA_938014855.1_SRR6713635_bin.11_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 00:45:52,638] [INFO] DFAST_QC completed!
[2023-06-13 00:45:52,638] [INFO] Total running time: 0h0m51s