[2023-06-28 23:08:48,056] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:08:48,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:08:48,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference
[2023-06-28 23:08:49,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:08:49,251] [INFO] Task started: Prodigal
[2023-06-28 23:08:49,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg72b0d89d-2c74-4b54-9688-c8889d5d051e/GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:08:52,425] [INFO] Task succeeded: Prodigal
[2023-06-28 23:08:52,425] [INFO] Task started: HMMsearch
[2023-06-28 23:08:52,426] [INFO] Running command: hmmsearch --tblout GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/reference_markers.hmm GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:08:52,657] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:08:52,659] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg72b0d89d-2c74-4b54-9688-c8889d5d051e/GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 23:08:52,677] [INFO] Query marker FASTA was written to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 23:08:52,677] [INFO] Task started: Blastn
[2023-06-28 23:08:52,677] [INFO] Running command: blastn -query GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/reference_markers.fasta -out GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:08:53,305] [INFO] Task succeeded: Blastn
[2023-06-28 23:08:53,310] [INFO] Selected 12 target genomes.
[2023-06-28 23:08:53,311] [INFO] Target genome list was writen to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 23:08:53,315] [INFO] Task started: fastANI
[2023-06-28 23:08:53,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg72b0d89d-2c74-4b54-9688-c8889d5d051e/GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:09:00,079] [INFO] Task succeeded: fastANI
[2023-06-28 23:09:00,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:09:00,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:09:00,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:09:00,082] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:09:00,082] [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 23:09:00,084] [INFO] DFAST Taxonomy check result was written to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 23:09:00,085] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:09:00,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:09:00,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/checkm_data
[2023-06-28 23:09:00,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:09:00,109] [INFO] Task started: CheckM
[2023-06-28 23:09:00,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 23:09:17,279] [INFO] Task succeeded: CheckM
[2023-06-28 23:09:17,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:09:17,301] [INFO] ===== Completeness check finished =====
[2023-06-28 23:09:17,302] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:09:17,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 23:09:17,302] [INFO] Task started: Blastn
[2023-06-28 23:09:17,303] [INFO] Running command: blastn -query GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg32a00a94-3a16-46a9-a020-610c8f513be1/dqc_reference/reference_markers_gtdb.fasta -out GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:09:18,289] [INFO] Task succeeded: Blastn
[2023-06-28 23:09:18,294] [INFO] Selected 16 target genomes.
[2023-06-28 23:09:18,294] [INFO] Target genome list was writen to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:09:18,308] [INFO] Task started: fastANI
[2023-06-28 23:09:18,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg72b0d89d-2c74-4b54-9688-c8889d5d051e/GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:09:25,258] [INFO] Task succeeded: fastANI
[2023-06-28 23:09:25,265] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:09:25,266] [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_002338345.1	s__UBA1859 sp002338345	99.2302	229	375	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003532555.1	s__UBA1859 sp003532555	85.3307	192	375	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691095.1	s__UBA1859 sp002691095	80.6774	161	375	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	98.96	98.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-28 23:09:25,268] [INFO] GTDB search result was written to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 23:09:25,269] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:09:25,272] [INFO] DFAST_QC result json was written to GCA_913065005.1_ERR2098388_bin.74_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 23:09:25,272] [INFO] DFAST_QC completed!
[2023-06-28 23:09:25,272] [INFO] Total running time: 0h0m37s