[2023-06-13 12:09:30,931] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:09:30,933] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:09:30,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference
[2023-06-13 12:09:33,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:09:33,495] [INFO] Task started: Prodigal
[2023-06-13 12:09:33,496] [INFO] Running command: gunzip -c /var/lib/cwl/stgd50da3d5-dd1b-4ebf-a881-9c3fcbc726a6/GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:09:36,717] [INFO] Task succeeded: Prodigal
[2023-06-13 12:09:36,718] [INFO] Task started: HMMsearch
[2023-06-13 12:09:36,718] [INFO] Running command: hmmsearch --tblout GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/reference_markers.hmm GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:09:36,948] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:09:36,951] [INFO] Found 6/6 markers.
[2023-06-13 12:09:36,975] [INFO] Query marker FASTA was written to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 12:09:36,975] [INFO] Task started: Blastn
[2023-06-13 12:09:36,975] [INFO] Running command: blastn -query GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/reference_markers.fasta -out GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:09:38,051] [INFO] Task succeeded: Blastn
[2023-06-13 12:09:38,056] [INFO] Selected 29 target genomes.
[2023-06-13 12:09:38,056] [INFO] Target genome list was writen to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 12:09:38,073] [INFO] Task started: fastANI
[2023-06-13 12:09:38,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50da3d5-dd1b-4ebf-a881-9c3fcbc726a6/GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:09:51,656] [INFO] Task succeeded: fastANI
[2023-06-13 12:09:51,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:09:51,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:09:51,666] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:09:51,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 12:09:51,666] [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
Defluviitalea raffinosedens	strain=DSM 28090	GCA_016908775.1	1450156	1450156	type	True	76.3645	57	638	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	76.3211	120	638	95	below_threshold
Natranaerovirga pectinivora	strain=DSM 24629	GCA_004342165.1	682400	682400	type	True	75.9597	54	638	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:09:51,669] [INFO] DFAST Taxonomy check result was written to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 12:09:51,669] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:09:51,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:09:51,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/checkm_data
[2023-06-13 12:09:51,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:09:51,699] [INFO] Task started: CheckM
[2023-06-13 12:09:51,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 12:10:09,645] [INFO] Task succeeded: CheckM
[2023-06-13 12:10:09,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 12:10:09,677] [INFO] ===== Completeness check finished =====
[2023-06-13 12:10:09,677] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:10:09,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 12:10:09,678] [INFO] Task started: Blastn
[2023-06-13 12:10:09,678] [INFO] Running command: blastn -query GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg48dbb098-bf58-4482-9eb3-3c3df5f17cef/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:10:10,396] [INFO] Task succeeded: Blastn
[2023-06-13 12:10:10,400] [INFO] Selected 23 target genomes.
[2023-06-13 12:10:10,400] [INFO] Target genome list was writen to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:10:10,417] [INFO] Task started: fastANI
[2023-06-13 12:10:10,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50da3d5-dd1b-4ebf-a881-9c3fcbc726a6/GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:10:21,126] [INFO] Task succeeded: fastANI
[2023-06-13 12:10:21,138] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:10:21,139] [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_012524135.1	s__JAAYNZ01 sp012524135	99.5653	472	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__JAAYNZ01;g__JAAYNZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012520595.1	s__JAAYNZ01 sp012520595	79.6442	355	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__JAAYNZ01;g__JAAYNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799415.1	s__JAAZLH01 sp012799415	77.4331	201	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__JAAYNZ01;g__JAAZLH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908775.1	s__Defluviitalea_A raffinosedens	76.3645	57	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	99.48	99.46	0.95	0.94	3	-
GCF_001466305.1	s__Defluviitalea phaphyphila	76.3211	120	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518815.1	s__JAAYML01 sp012518815	76.2311	70	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521175.1	s__Defluviitalea_A sp012521175	75.8686	53	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:10:21,141] [INFO] GTDB search result was written to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 12:10:21,142] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:10:21,146] [INFO] DFAST_QC result json was written to GCA_938014895.1_SRR6713635_bin.66_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 12:10:21,146] [INFO] DFAST_QC completed!
[2023-06-13 12:10:21,146] [INFO] Total running time: 0h0m50s