[2023-06-28 23:29:01,583] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:29:01,586] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:29:01,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference
[2023-06-28 23:29:02,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:29:02,792] [INFO] Task started: Prodigal
[2023-06-28 23:29:02,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8e5c9e0-cffb-41a5-a6fa-47d59315b9e2/GCA_944322185.1_E40_bin232_genomic.fna.gz | prodigal -d GCA_944322185.1_E40_bin232_genomic.fna/cds.fna -a GCA_944322185.1_E40_bin232_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:29:07,360] [INFO] Task succeeded: Prodigal
[2023-06-28 23:29:07,361] [INFO] Task started: HMMsearch
[2023-06-28 23:29:07,361] [INFO] Running command: hmmsearch --tblout GCA_944322185.1_E40_bin232_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/reference_markers.hmm GCA_944322185.1_E40_bin232_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:29:07,597] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:29:07,599] [INFO] Found 6/6 markers.
[2023-06-28 23:29:07,623] [INFO] Query marker FASTA was written to GCA_944322185.1_E40_bin232_genomic.fna/markers.fasta
[2023-06-28 23:29:07,623] [INFO] Task started: Blastn
[2023-06-28 23:29:07,624] [INFO] Running command: blastn -query GCA_944322185.1_E40_bin232_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/reference_markers.fasta -out GCA_944322185.1_E40_bin232_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:29:08,226] [INFO] Task succeeded: Blastn
[2023-06-28 23:29:08,230] [INFO] Selected 25 target genomes.
[2023-06-28 23:29:08,231] [INFO] Target genome list was writen to GCA_944322185.1_E40_bin232_genomic.fna/target_genomes.txt
[2023-06-28 23:29:08,239] [INFO] Task started: fastANI
[2023-06-28 23:29:08,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8e5c9e0-cffb-41a5-a6fa-47d59315b9e2/GCA_944322185.1_E40_bin232_genomic.fna.gz --refList GCA_944322185.1_E40_bin232_genomic.fna/target_genomes.txt --output GCA_944322185.1_E40_bin232_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:29:21,107] [INFO] Task succeeded: fastANI
[2023-06-28 23:29:21,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:29:21,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:29:21,110] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:29:21,110] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:29:21,110] [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
--------------------------------------------------------------------------------
[2023-06-28 23:29:21,112] [INFO] DFAST Taxonomy check result was written to GCA_944322185.1_E40_bin232_genomic.fna/tc_result.tsv
[2023-06-28 23:29:21,113] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:29:21,113] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:29:21,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/checkm_data
[2023-06-28 23:29:21,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:29:21,142] [INFO] Task started: CheckM
[2023-06-28 23:29:21,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322185.1_E40_bin232_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322185.1_E40_bin232_genomic.fna/checkm_input GCA_944322185.1_E40_bin232_genomic.fna/checkm_result
[2023-06-28 23:29:41,621] [INFO] Task succeeded: CheckM
[2023-06-28 23:29:41,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:29:41,641] [INFO] ===== Completeness check finished =====
[2023-06-28 23:29:41,641] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:29:41,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322185.1_E40_bin232_genomic.fna/markers.fasta)
[2023-06-28 23:29:41,642] [INFO] Task started: Blastn
[2023-06-28 23:29:41,642] [INFO] Running command: blastn -query GCA_944322185.1_E40_bin232_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bc0c7d-8100-435b-a5ab-d22624eed1fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322185.1_E40_bin232_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:29:42,456] [INFO] Task succeeded: Blastn
[2023-06-28 23:29:42,460] [INFO] Selected 12 target genomes.
[2023-06-28 23:29:42,460] [INFO] Target genome list was writen to GCA_944322185.1_E40_bin232_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:29:42,471] [INFO] Task started: fastANI
[2023-06-28 23:29:42,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8e5c9e0-cffb-41a5-a6fa-47d59315b9e2/GCA_944322185.1_E40_bin232_genomic.fna.gz --refList GCA_944322185.1_E40_bin232_genomic.fna/target_genomes_gtdb.txt --output GCA_944322185.1_E40_bin232_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:29:46,196] [INFO] Task succeeded: fastANI
[2023-06-28 23:29:46,211] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:29:46,211] [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
GCA_900548955.1	s__CAG-1427 sp900548955	97.6677	412	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.92	99.92	0.92	0.92	2	conclusive
GCA_900542065.1	s__CAG-1427 sp000431675	88.9022	468	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.98	99.97	0.99	0.98	3	-
GCA_900551155.1	s__CAG-1427 sp900551155	87.4033	358	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	98.93	98.93	0.80	0.80	2	-
GCA_000435475.1	s__CAG-1427 sp000435475	81.539	287	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	96.89	96.41	0.87	0.87	4	-
GCA_900556585.1	s__CAG-1427 sp900556585	80.2229	163	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	98.47	98.45	0.84	0.83	3	-
GCA_900547965.1	s__CAG-1427 sp900547965	78.6539	77	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.87	99.87	0.90	0.90	2	-
GCA_900554685.1	s__CAG-1427 sp900554685	78.4972	193	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.84	99.84	0.88	0.88	2	-
GCA_900539675.1	s__CAG-1427 sp900539675	78.2782	152	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434775.1	s__CAG-1427 sp000434775	77.4145	84	604	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	98.66	98.56	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-28 23:29:46,213] [INFO] GTDB search result was written to GCA_944322185.1_E40_bin232_genomic.fna/result_gtdb.tsv
[2023-06-28 23:29:46,214] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:29:46,217] [INFO] DFAST_QC result json was written to GCA_944322185.1_E40_bin232_genomic.fna/dqc_result.json
[2023-06-28 23:29:46,217] [INFO] DFAST_QC completed!
[2023-06-28 23:29:46,218] [INFO] Total running time: 0h0m45s