[2023-06-13 05:35:16,827] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:35:16,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:35:16,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference
[2023-06-13 05:35:18,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:35:18,122] [INFO] Task started: Prodigal
[2023-06-13 05:35:18,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ccd06de-7a85-48a0-8c5b-203c6809ecdd/GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:35:22,209] [INFO] Task succeeded: Prodigal
[2023-06-13 05:35:22,209] [INFO] Task started: HMMsearch
[2023-06-13 05:35:22,210] [INFO] Running command: hmmsearch --tblout GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/reference_markers.hmm GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:35:22,437] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:35:22,438] [INFO] Found 6/6 markers.
[2023-06-13 05:35:22,464] [INFO] Query marker FASTA was written to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 05:35:22,465] [INFO] Task started: Blastn
[2023-06-13 05:35:22,465] [INFO] Running command: blastn -query GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/reference_markers.fasta -out GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:23,055] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:23,059] [INFO] Selected 28 target genomes.
[2023-06-13 05:35:23,059] [INFO] Target genome list was writen to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:35:23,066] [INFO] Task started: fastANI
[2023-06-13 05:35:23,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ccd06de-7a85-48a0-8c5b-203c6809ecdd/GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:35:39,252] [INFO] Task succeeded: fastANI
[2023-06-13 05:35:39,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:35:39,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:35:39,255] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:35:39,255] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:35:39,256] [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
--------------------------------------------------------------------------------
[2023-06-13 05:35:39,258] [INFO] DFAST Taxonomy check result was written to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:35:39,259] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:35:39,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:35:39,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/checkm_data
[2023-06-13 05:35:39,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:35:39,284] [INFO] Task started: CheckM
[2023-06-13 05:35:39,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 05:35:58,575] [INFO] Task succeeded: CheckM
[2023-06-13 05:35:58,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:35:58,598] [INFO] ===== Completeness check finished =====
[2023-06-13 05:35:58,598] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:35:58,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:35:58,599] [INFO] Task started: Blastn
[2023-06-13 05:35:58,599] [INFO] Running command: blastn -query GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a09ae4c-ceea-4137-a379-e60fc2e1fa95/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:59,445] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:59,450] [INFO] Selected 18 target genomes.
[2023-06-13 05:35:59,450] [INFO] Target genome list was writen to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:35:59,461] [INFO] Task started: fastANI
[2023-06-13 05:35:59,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ccd06de-7a85-48a0-8c5b-203c6809ecdd/GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:36:05,195] [INFO] Task succeeded: fastANI
[2023-06-13 05:36:05,211] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:36:05,211] [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_904387375.1	s__Protoclostridium gallicola	98.2469	468	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	99.11	98.28	0.95	0.92	3	conclusive
GCA_900555875.1	s__Protoclostridium sp900555875	79.6567	91	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761765.1	s__Protoclostridium sp900761765	79.2262	192	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113275.1	s__Protoclostridium stercorigallinarum	78.6147	139	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587025.1	s__Protoclostridium sp910587025	78.2222	135	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113265.1	s__Protoclostridium sp019113265	77.9166	147	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017452405.1	s__Protoclostridium sp017452405	77.4302	58	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761915.1	s__HGM11386 sp900761915	77.0471	50	510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__HGM11386	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:36:05,213] [INFO] GTDB search result was written to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:36:05,214] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:36:05,219] [INFO] DFAST_QC result json was written to GCA_938048205.1_ERR321597_bin.55_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:36:05,219] [INFO] DFAST_QC completed!
[2023-06-13 05:36:05,219] [INFO] Total running time: 0h0m48s