[2023-06-30 17:53:35,619] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:53:35,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:53:35,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference
[2023-06-30 17:53:37,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:53:37,510] [INFO] Task started: Prodigal
[2023-06-30 17:53:37,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cb3160b-ccf6-49f1-a00e-128f8c0f67a1/GCA_016926975.1_ASM1692697v1_genomic.fna.gz | prodigal -d GCA_016926975.1_ASM1692697v1_genomic.fna/cds.fna -a GCA_016926975.1_ASM1692697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:53:41,508] [INFO] Task succeeded: Prodigal
[2023-06-30 17:53:41,508] [INFO] Task started: HMMsearch
[2023-06-30 17:53:41,508] [INFO] Running command: hmmsearch --tblout GCA_016926975.1_ASM1692697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/reference_markers.hmm GCA_016926975.1_ASM1692697v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:53:41,724] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:53:41,725] [INFO] Found 6/6 markers.
[2023-06-30 17:53:41,743] [INFO] Query marker FASTA was written to GCA_016926975.1_ASM1692697v1_genomic.fna/markers.fasta
[2023-06-30 17:53:41,743] [INFO] Task started: Blastn
[2023-06-30 17:53:41,743] [INFO] Running command: blastn -query GCA_016926975.1_ASM1692697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/reference_markers.fasta -out GCA_016926975.1_ASM1692697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:53:42,348] [INFO] Task succeeded: Blastn
[2023-06-30 17:53:42,352] [INFO] Selected 31 target genomes.
[2023-06-30 17:53:42,352] [INFO] Target genome list was writen to GCA_016926975.1_ASM1692697v1_genomic.fna/target_genomes.txt
[2023-06-30 17:53:42,360] [INFO] Task started: fastANI
[2023-06-30 17:53:42,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb3160b-ccf6-49f1-a00e-128f8c0f67a1/GCA_016926975.1_ASM1692697v1_genomic.fna.gz --refList GCA_016926975.1_ASM1692697v1_genomic.fna/target_genomes.txt --output GCA_016926975.1_ASM1692697v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:54:03,980] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:03,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:54:03,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:54:03,982] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:54:03,983] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:54:03,983] [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
--------------------------------------------------------------------------------
[2023-06-30 17:54:03,984] [INFO] DFAST Taxonomy check result was written to GCA_016926975.1_ASM1692697v1_genomic.fna/tc_result.tsv
[2023-06-30 17:54:03,985] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:54:03,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:54:03,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/checkm_data
[2023-06-30 17:54:03,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:54:04,011] [INFO] Task started: CheckM
[2023-06-30 17:54:04,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016926975.1_ASM1692697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016926975.1_ASM1692697v1_genomic.fna/checkm_input GCA_016926975.1_ASM1692697v1_genomic.fna/checkm_result
[2023-06-30 17:54:20,952] [INFO] Task succeeded: CheckM
[2023-06-30 17:54:20,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:54:20,970] [INFO] ===== Completeness check finished =====
[2023-06-30 17:54:20,970] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:54:20,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016926975.1_ASM1692697v1_genomic.fna/markers.fasta)
[2023-06-30 17:54:20,970] [INFO] Task started: Blastn
[2023-06-30 17:54:20,971] [INFO] Running command: blastn -query GCA_016926975.1_ASM1692697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg558aabc0-fd4f-423b-b06e-18e11ed27457/dqc_reference/reference_markers_gtdb.fasta -out GCA_016926975.1_ASM1692697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:21,843] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:21,846] [INFO] Selected 18 target genomes.
[2023-06-30 17:54:21,846] [INFO] Target genome list was writen to GCA_016926975.1_ASM1692697v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:54:21,888] [INFO] Task started: fastANI
[2023-06-30 17:54:21,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb3160b-ccf6-49f1-a00e-128f8c0f67a1/GCA_016926975.1_ASM1692697v1_genomic.fna.gz --refList GCA_016926975.1_ASM1692697v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016926975.1_ASM1692697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:54:29,594] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:29,602] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:54:29,603] [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_016926975.1	s__UBA6100 sp016926975	100.0	471	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA6100	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002423585.1	s__UBA6100 sp002423585	79.5846	242	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA6100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009668945.1	s__UBA6100 sp009668945	79.0444	206	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA6100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328745.1	s__UBA2184 sp002328745	78.8249	195	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA2184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015351705.1	s__JADIIM01 sp015351705	78.739	186	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__JADIIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938395.1	s__UBA2272 sp016938395	78.6644	170	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA2272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347725.1	s__UBA2272 sp002347725	78.5812	195	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA2272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453535.1	s__UBA7930 sp003453535	78.5301	181	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA7930	95.0	99.85	99.85	0.89	0.89	2	-
GCA_011372845.1	s__UBA7930 sp011372845	78.2933	95	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA7930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933785.1	s__UBA7930 sp016933785	78.2135	146	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA7930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841295.1	s__UBA2286 sp002841295	77.0342	91	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA2286	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331305.1	s__DSSC01 sp011331305	76.845	73	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__PHET01;g__DSSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859305.1	s__Kmv31 sp014859305	76.7804	89	474	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__Kmv31;g__Kmv31	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:54:29,604] [INFO] GTDB search result was written to GCA_016926975.1_ASM1692697v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:54:29,605] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:54:29,607] [INFO] DFAST_QC result json was written to GCA_016926975.1_ASM1692697v1_genomic.fna/dqc_result.json
[2023-06-30 17:54:29,607] [INFO] DFAST_QC completed!
[2023-06-30 17:54:29,608] [INFO] Total running time: 0h0m54s