[2023-06-08 13:33:41,785] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:41,786] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:41,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference
[2023-06-08 13:33:42,877] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:42,878] [INFO] Task started: Prodigal
[2023-06-08 13:33:42,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg833542f6-b462-47be-b977-153f085a3fed/GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna.gz | prodigal -d GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/cds.fna -a GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:48,988] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:48,988] [INFO] Task started: HMMsearch
[2023-06-08 13:33:48,988] [INFO] Running command: hmmsearch --tblout GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/reference_markers.hmm GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:49,155] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:49,156] [INFO] Found 6/6 markers.
[2023-06-08 13:33:49,178] [INFO] Query marker FASTA was written to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 13:33:49,178] [INFO] Task started: Blastn
[2023-06-08 13:33:49,178] [INFO] Running command: blastn -query GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/reference_markers.fasta -out GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:49,694] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:49,697] [INFO] Selected 5 target genomes.
[2023-06-08 13:33:49,697] [INFO] Target genome list was writen to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 13:33:49,699] [INFO] Task started: fastANI
[2023-06-08 13:33:49,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg833542f6-b462-47be-b977-153f085a3fed/GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna.gz --refList GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:52,237] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:52,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:52,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:52,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:52,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:33:52,242] [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
--------------------------------------------------------------------------------
[2023-06-08 13:33:52,243] [INFO] DFAST Taxonomy check result was written to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 13:33:52,244] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:52,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:52,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/checkm_data
[2023-06-08 13:33:52,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:52,274] [INFO] Task started: CheckM
[2023-06-08 13:33:52,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/checkm_input GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/checkm_result
[2023-06-08 13:34:14,902] [INFO] Task succeeded: CheckM
[2023-06-08 13:34:14,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:34:14,920] [INFO] ===== Completeness check finished =====
[2023-06-08 13:34:14,920] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:34:14,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 13:34:14,920] [INFO] Task started: Blastn
[2023-06-08 13:34:14,920] [INFO] Running command: blastn -query GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b8ae03-a225-4fbc-bd1a-d2daa3180249/dqc_reference/reference_markers_gtdb.fasta -out GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:34:15,648] [INFO] Task succeeded: Blastn
[2023-06-08 13:34:15,651] [INFO] Selected 16 target genomes.
[2023-06-08 13:34:15,652] [INFO] Target genome list was writen to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:34:15,829] [INFO] Task started: fastANI
[2023-06-08 13:34:15,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg833542f6-b462-47be-b977-153f085a3fed/GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna.gz --refList GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:34:21,762] [INFO] Task succeeded: fastANI
[2023-06-08 13:34:21,767] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:34:21,768] [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_013204545.1	s__UBA1328 sp013204545	99.6648	805	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018649665.1	s__UBA1328 sp018649665	78.5714	308	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650845.1	s__UBA1328 sp018650845	78.4236	314	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_018673955.1	s__UBA1328 sp018673955	78.1262	256	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
GCA_905614375.1	s__UBA1328 sp905614375	78.0309	141	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959765.1	s__UBA1328 sp012959765	77.6781	282	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_002501045.1	s__UBA1328 sp002501045	77.4618	205	869	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-08 13:34:21,777] [INFO] GTDB search result was written to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 13:34:21,778] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:34:21,780] [INFO] DFAST_QC result json was written to GCA_902752465.1_P2236_102_bin76_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 13:34:21,780] [INFO] DFAST_QC completed!
[2023-06-08 13:34:21,780] [INFO] Total running time: 0h0m40s