[2023-06-05 05:15:47,010] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:47,017] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:47,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference
[2023-06-05 05:15:48,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:48,216] [INFO] Task started: Prodigal
[2023-06-05 05:15:48,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgb30a33f3-13b8-47b4-a90b-9eb7b4443970/GCA_934643825.1_ERR7738959_bin.395_genomic.fna.gz | prodigal -d GCA_934643825.1_ERR7738959_bin.395_genomic.fna/cds.fna -a GCA_934643825.1_ERR7738959_bin.395_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:55,041] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:55,042] [INFO] Task started: HMMsearch
[2023-06-05 05:15:55,042] [INFO] Running command: hmmsearch --tblout GCA_934643825.1_ERR7738959_bin.395_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/reference_markers.hmm GCA_934643825.1_ERR7738959_bin.395_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:55,295] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:55,296] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb30a33f3-13b8-47b4-a90b-9eb7b4443970/GCA_934643825.1_ERR7738959_bin.395_genomic.fna.gz]
[2023-06-05 05:15:55,328] [INFO] Query marker FASTA was written to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/markers.fasta
[2023-06-05 05:15:55,329] [INFO] Task started: Blastn
[2023-06-05 05:15:55,329] [INFO] Running command: blastn -query GCA_934643825.1_ERR7738959_bin.395_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/reference_markers.fasta -out GCA_934643825.1_ERR7738959_bin.395_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:55,956] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:55,961] [INFO] Selected 25 target genomes.
[2023-06-05 05:15:55,961] [INFO] Target genome list was writen to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/target_genomes.txt
[2023-06-05 05:15:55,963] [INFO] Task started: fastANI
[2023-06-05 05:15:55,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgb30a33f3-13b8-47b4-a90b-9eb7b4443970/GCA_934643825.1_ERR7738959_bin.395_genomic.fna.gz --refList GCA_934643825.1_ERR7738959_bin.395_genomic.fna/target_genomes.txt --output GCA_934643825.1_ERR7738959_bin.395_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:16:13,154] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:13,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:16:13,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:16:13,157] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:16:13,158] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:16:13,158] [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
--------------------------------------------------------------------------------
[2023-06-05 05:16:13,160] [INFO] DFAST Taxonomy check result was written to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/tc_result.tsv
[2023-06-05 05:16:13,161] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:16:13,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:16:13,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/checkm_data
[2023-06-05 05:16:13,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:16:13,211] [INFO] Task started: CheckM
[2023-06-05 05:16:13,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934643825.1_ERR7738959_bin.395_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934643825.1_ERR7738959_bin.395_genomic.fna/checkm_input GCA_934643825.1_ERR7738959_bin.395_genomic.fna/checkm_result
[2023-06-05 05:16:39,651] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:39,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:39,674] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:39,674] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:39,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934643825.1_ERR7738959_bin.395_genomic.fna/markers.fasta)
[2023-06-05 05:16:39,675] [INFO] Task started: Blastn
[2023-06-05 05:16:39,675] [INFO] Running command: blastn -query GCA_934643825.1_ERR7738959_bin.395_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee130bf-0fc6-4c61-8f48-80d4af809645/dqc_reference/reference_markers_gtdb.fasta -out GCA_934643825.1_ERR7738959_bin.395_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:40,569] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:40,573] [INFO] Selected 11 target genomes.
[2023-06-05 05:16:40,574] [INFO] Target genome list was writen to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:40,576] [INFO] Task started: fastANI
[2023-06-05 05:16:40,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgb30a33f3-13b8-47b4-a90b-9eb7b4443970/GCA_934643825.1_ERR7738959_bin.395_genomic.fna.gz --refList GCA_934643825.1_ERR7738959_bin.395_genomic.fna/target_genomes_gtdb.txt --output GCA_934643825.1_ERR7738959_bin.395_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:16:46,501] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:46,513] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 05:16:46,513] [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_900548125.1	s__Ventricola sp900548125	92.5411	415	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.02	96.93	0.87	0.87	4	-
GCA_900542395.1	s__Ventricola sp900542395	82.3159	429	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.33	97.06	0.84	0.79	5	-
GCA_900542445.1	s__Ventricola sp900542445	82.1993	450	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.97	98.40	0.91	0.87	4	-
GCA_004555535.1	s__Ventricola sp004555535	79.1078	295	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556985.1	s__Ventricola sp004556985	78.9047	271	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521565.1	s__Ventricola sp017521565	78.639	233	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937505.1	s__Ventricola sp017937505	78.6108	260	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938795.1	s__Ventricola sp017938795	78.2418	215	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550745.1	s__RUG563 sp017550745	76.7892	51	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG563	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:16:46,515] [INFO] GTDB search result was written to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/result_gtdb.tsv
[2023-06-05 05:16:46,516] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:16:46,519] [INFO] DFAST_QC result json was written to GCA_934643825.1_ERR7738959_bin.395_genomic.fna/dqc_result.json
[2023-06-05 05:16:46,519] [INFO] DFAST_QC completed!
[2023-06-05 05:16:46,519] [INFO] Total running time: 0h0m60s