[2023-06-28 12:49:23,849] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:23,854] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:23,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference
[2023-06-28 12:49:25,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:25,185] [INFO] Task started: Prodigal
[2023-06-28 12:49:25,186] [INFO] Running command: gunzip -c /var/lib/cwl/stg312f6edc-558c-496b-b350-07532f5032aa/GCA_944320375.1_BRZ_N_bin190_genomic.fna.gz | prodigal -d GCA_944320375.1_BRZ_N_bin190_genomic.fna/cds.fna -a GCA_944320375.1_BRZ_N_bin190_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:36,771] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:36,772] [INFO] Task started: HMMsearch
[2023-06-28 12:49:36,772] [INFO] Running command: hmmsearch --tblout GCA_944320375.1_BRZ_N_bin190_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/reference_markers.hmm GCA_944320375.1_BRZ_N_bin190_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:36,984] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:36,985] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg312f6edc-558c-496b-b350-07532f5032aa/GCA_944320375.1_BRZ_N_bin190_genomic.fna.gz]
[2023-06-28 12:49:37,009] [INFO] Query marker FASTA was written to GCA_944320375.1_BRZ_N_bin190_genomic.fna/markers.fasta
[2023-06-28 12:49:37,009] [INFO] Task started: Blastn
[2023-06-28 12:49:37,009] [INFO] Running command: blastn -query GCA_944320375.1_BRZ_N_bin190_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/reference_markers.fasta -out GCA_944320375.1_BRZ_N_bin190_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:37,536] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:37,541] [INFO] Selected 5 target genomes.
[2023-06-28 12:49:37,541] [INFO] Target genome list was writen to GCA_944320375.1_BRZ_N_bin190_genomic.fna/target_genomes.txt
[2023-06-28 12:49:37,543] [INFO] Task started: fastANI
[2023-06-28 12:49:37,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg312f6edc-558c-496b-b350-07532f5032aa/GCA_944320375.1_BRZ_N_bin190_genomic.fna.gz --refList GCA_944320375.1_BRZ_N_bin190_genomic.fna/target_genomes.txt --output GCA_944320375.1_BRZ_N_bin190_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:40,600] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:40,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:40,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:40,603] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:40,603] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:49:40,603] [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 12:49:40,605] [INFO] DFAST Taxonomy check result was written to GCA_944320375.1_BRZ_N_bin190_genomic.fna/tc_result.tsv
[2023-06-28 12:49:40,606] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:40,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:40,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/checkm_data
[2023-06-28 12:49:40,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:40,638] [INFO] Task started: CheckM
[2023-06-28 12:49:40,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320375.1_BRZ_N_bin190_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320375.1_BRZ_N_bin190_genomic.fna/checkm_input GCA_944320375.1_BRZ_N_bin190_genomic.fna/checkm_result
[2023-06-28 12:50:16,712] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:16,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:16,736] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:16,737] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:16,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320375.1_BRZ_N_bin190_genomic.fna/markers.fasta)
[2023-06-28 12:50:16,737] [INFO] Task started: Blastn
[2023-06-28 12:50:16,738] [INFO] Running command: blastn -query GCA_944320375.1_BRZ_N_bin190_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f36d00e-c89f-4349-b8c6-7cc219fc6830/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320375.1_BRZ_N_bin190_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:17,217] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:17,223] [INFO] Selected 7 target genomes.
[2023-06-28 12:50:17,223] [INFO] Target genome list was writen to GCA_944320375.1_BRZ_N_bin190_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:17,227] [INFO] Task started: fastANI
[2023-06-28 12:50:17,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg312f6edc-558c-496b-b350-07532f5032aa/GCA_944320375.1_BRZ_N_bin190_genomic.fna.gz --refList GCA_944320375.1_BRZ_N_bin190_genomic.fna/target_genomes_gtdb.txt --output GCA_944320375.1_BRZ_N_bin190_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:20,220] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:20,231] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:20,232] [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_009911715.1	s__UBA71 sp006954425	97.3145	510	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	96.86	96.86	0.82	0.82	2	conclusive
GCA_905187815.1	s__UBA71 sp905187815	85.5799	403	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504405.1	s__UBA71 sp002504405	82.0194	314	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461225.1	s__UBA71 sp017461225	81.4034	263	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767505.1	s__UBA71 sp900767505	81.1707	190	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063135.1	s__UBA71 sp015063135	80.7973	257	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	98.46	98.46	0.93	0.93	2	-
GCA_015063165.1	s__UBA71 sp015063165	79.7807	234	611	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	97.04	96.86	0.88	0.87	5	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:20,234] [INFO] GTDB search result was written to GCA_944320375.1_BRZ_N_bin190_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:20,235] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:20,238] [INFO] DFAST_QC result json was written to GCA_944320375.1_BRZ_N_bin190_genomic.fna/dqc_result.json
[2023-06-28 12:50:20,238] [INFO] DFAST_QC completed!
[2023-06-28 12:50:20,238] [INFO] Total running time: 0h0m56s