[2023-06-29 14:46:18,948] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:46:18,950] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:46:18,950] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference
[2023-06-29 14:46:20,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:46:20,480] [INFO] Task started: Prodigal
[2023-06-29 14:46:20,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg417c9269-884b-414f-bad3-ea916998e0de/GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:46:39,205] [INFO] Task succeeded: Prodigal
[2023-06-29 14:46:39,206] [INFO] Task started: HMMsearch
[2023-06-29 14:46:39,206] [INFO] Running command: hmmsearch --tblout GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/reference_markers.hmm GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:46:39,567] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:46:39,569] [INFO] Found 6/6 markers.
[2023-06-29 14:46:39,614] [INFO] Query marker FASTA was written to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:46:39,614] [INFO] Task started: Blastn
[2023-06-29 14:46:39,615] [INFO] Running command: blastn -query GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/reference_markers.fasta -out GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:46:40,235] [INFO] Task succeeded: Blastn
[2023-06-29 14:46:40,244] [INFO] Selected 29 target genomes.
[2023-06-29 14:46:40,245] [INFO] Target genome list was writen to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:46:40,248] [INFO] Task started: fastANI
[2023-06-29 14:46:40,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg417c9269-884b-414f-bad3-ea916998e0de/GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:47:01,739] [INFO] Task succeeded: fastANI
[2023-06-29 14:47:01,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:47:01,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:47:01,743] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:47:01,744] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:47:01,744] [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
--------------------------------------------------------------------------------
[2023-06-29 14:47:01,747] [INFO] DFAST Taxonomy check result was written to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:47:01,748] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:47:01,748] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:47:01,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/checkm_data
[2023-06-29 14:47:01,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:47:01,802] [INFO] Task started: CheckM
[2023-06-29 14:47:01,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:47:56,577] [INFO] Task succeeded: CheckM
[2023-06-29 14:47:56,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.87%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-29 14:47:56,607] [INFO] ===== Completeness check finished =====
[2023-06-29 14:47:56,607] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:47:56,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:47:56,608] [INFO] Task started: Blastn
[2023-06-29 14:47:56,608] [INFO] Running command: blastn -query GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1df57ca-c75b-4c51-9464-2777afe62693/dqc_reference/reference_markers_gtdb.fasta -out GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:47:57,382] [INFO] Task succeeded: Blastn
[2023-06-29 14:47:57,387] [INFO] Selected 12 target genomes.
[2023-06-29 14:47:57,388] [INFO] Target genome list was writen to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:47:57,392] [INFO] Task started: fastANI
[2023-06-29 14:47:57,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg417c9269-884b-414f-bad3-ea916998e0de/GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:48:04,982] [INFO] Task succeeded: fastANI
[2023-06-29 14:48:04,992] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:48:04,993] [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_016709575.1	s__JAFLBH01 sp016709575	80.0454	695	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018000995.1	s__JAFLBH01 sp018000995	80.0121	669	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303905.1	s__JAFLBH01 sp017303905	77.6745	288	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787705.1	s__UBA2475 sp016787705	77.6114	164	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705695.1	s__UBA2475 sp016705695	77.5062	156	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	96.82	95.10	0.91	0.90	4	-
GCA_016787445.1	s__JAFLBH01 sp016787445	77.3057	283	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342065.1	s__UBA2475 sp002342065	76.9362	170	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697245.1	s__UBA2475 sp013697245	76.7071	145	1595	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:48:04,995] [INFO] GTDB search result was written to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:48:04,995] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:48:04,998] [INFO] DFAST_QC result json was written to GCA_937873155.1_SRR6670123_bin.16_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:48:04,998] [INFO] DFAST_QC completed!
[2023-06-29 14:48:04,999] [INFO] Total running time: 0h1m46s