[2023-06-13 14:45:32,757] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:32,760] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:32,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference
[2023-06-13 14:45:33,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:33,996] [INFO] Task started: Prodigal
[2023-06-13 14:45:33,996] [INFO] Running command: gunzip -c /var/lib/cwl/stge5278617-6be6-4365-ad61-4f04968fa413/GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:46,072] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:46,072] [INFO] Task started: HMMsearch
[2023-06-13 14:45:46,072] [INFO] Running command: hmmsearch --tblout GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/reference_markers.hmm GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:46,327] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:46,328] [INFO] Found 6/6 markers.
[2023-06-13 14:45:46,355] [INFO] Query marker FASTA was written to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:45:46,355] [INFO] Task started: Blastn
[2023-06-13 14:45:46,355] [INFO] Running command: blastn -query GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/reference_markers.fasta -out GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:46,904] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:46,907] [INFO] Selected 17 target genomes.
[2023-06-13 14:45:46,907] [INFO] Target genome list was writen to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:45:46,908] [INFO] Task started: fastANI
[2023-06-13 14:45:46,908] [INFO] Running command: fastANI --query /var/lib/cwl/stge5278617-6be6-4365-ad61-4f04968fa413/GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:57,701] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:57,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:57,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:57,707] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:45:57,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:45:57,708] [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
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	93.4658	1012	1145	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	93.4477	1020	1145	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	80.0637	82	1145	95	below_threshold
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	77.2982	161	1145	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	76.1541	50	1145	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	76.153	50	1145	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:45:57,709] [INFO] DFAST Taxonomy check result was written to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:45:57,710] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:57,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:57,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/checkm_data
[2023-06-13 14:45:57,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:57,747] [INFO] Task started: CheckM
[2023-06-13 14:45:57,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:46:33,587] [INFO] Task succeeded: CheckM
[2023-06-13 14:46:33,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:46:33,603] [INFO] ===== Completeness check finished =====
[2023-06-13 14:46:33,603] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:46:33,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:46:33,604] [INFO] Task started: Blastn
[2023-06-13 14:46:33,604] [INFO] Running command: blastn -query GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf88d7a-83d1-4778-8012-050fa182e7f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:34,334] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:34,337] [INFO] Selected 19 target genomes.
[2023-06-13 14:46:34,337] [INFO] Target genome list was writen to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:46:34,342] [INFO] Task started: fastANI
[2023-06-13 14:46:34,342] [INFO] Running command: fastANI --query /var/lib/cwl/stge5278617-6be6-4365-ad61-4f04968fa413/GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:46:45,211] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:45,217] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:46:45,217] [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_900545915.1	s__Coprobacter sp900545915	99.9759	1057	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.49	96.20	0.84	0.83	3	conclusive
GCF_003634345.1	s__Coprobacter fastidiosus	93.4477	1020	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	98.46	97.98	0.89	0.59	13	-
GCF_000296465.1	s__Barnesiella intestinihominis	79.9936	84	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	-
GCA_000803105.1	s__Coprobacter secundus	77.2889	146	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.96	96.86	0.90	0.85	6	-
GCA_017467745.1	s__Gallibacteroides sp017467745	76.7034	64	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CHK158-818;g__Gallibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434215.1	s__UBA11471 sp000434215	76.6316	60	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-13 14:46:45,218] [INFO] GTDB search result was written to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:46:45,219] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:46:45,221] [INFO] DFAST_QC result json was written to GCA_938017495.1_ERR589530_bin.38_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:46:45,221] [INFO] DFAST_QC completed!
[2023-06-13 14:46:45,221] [INFO] Total running time: 0h1m12s