[2023-06-08 11:59:43,122] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:59:43,124] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:59:43,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference
[2023-06-08 11:59:44,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:59:44,368] [INFO] Task started: Prodigal
[2023-06-08 11:59:44,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b8064e5-a22e-4fe8-ae6d-6e4a577d8079/GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:59:46,226] [INFO] Task succeeded: Prodigal
[2023-06-08 11:59:46,226] [INFO] Task started: HMMsearch
[2023-06-08 11:59:46,227] [INFO] Running command: hmmsearch --tblout GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/reference_markers.hmm GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:59:46,453] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:59:46,455] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4b8064e5-a22e-4fe8-ae6d-6e4a577d8079/GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 11:59:46,480] [INFO] Query marker FASTA was written to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:59:46,481] [INFO] Task started: Blastn
[2023-06-08 11:59:46,481] [INFO] Running command: blastn -query GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/reference_markers.fasta -out GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:59:47,096] [INFO] Task succeeded: Blastn
[2023-06-08 11:59:47,100] [INFO] Selected 25 target genomes.
[2023-06-08 11:59:47,100] [INFO] Target genome list was writen to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:59:47,103] [INFO] Task started: fastANI
[2023-06-08 11:59:47,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8064e5-a22e-4fe8-ae6d-6e4a577d8079/GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:59:57,813] [INFO] Task succeeded: fastANI
[2023-06-08 11:59:57,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:59:57,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:59:57,816] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:59:57,816] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:59:57,816] [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
--------------------------------------------------------------------------------
[2023-06-08 11:59:57,818] [INFO] DFAST Taxonomy check result was written to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:59:57,819] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:59:57,819] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:59:57,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/checkm_data
[2023-06-08 11:59:57,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:59:57,842] [INFO] Task started: CheckM
[2023-06-08 11:59:57,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:00:12,261] [INFO] Task succeeded: CheckM
[2023-06-08 12:00:12,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:00:12,279] [INFO] ===== Completeness check finished =====
[2023-06-08 12:00:12,280] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:00:12,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:00:12,281] [INFO] Task started: Blastn
[2023-06-08 12:00:12,281] [INFO] Running command: blastn -query GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf85fd39-8592-4ee1-a9e5-a2e83a70d42e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:00:13,153] [INFO] Task succeeded: Blastn
[2023-06-08 12:00:13,159] [INFO] Selected 19 target genomes.
[2023-06-08 12:00:13,159] [INFO] Target genome list was writen to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:00:13,164] [INFO] Task started: fastANI
[2023-06-08 12:00:13,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8064e5-a22e-4fe8-ae6d-6e4a577d8079/GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:00:17,782] [INFO] Task succeeded: fastANI
[2023-06-08 12:00:17,798] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:00:17,798] [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_017626365.1	s__RGIG8482 sp017626365	81.1527	252	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904381285.1	s__RGIG8482 sp904381285	79.6228	209	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198755.1	s__HGM13634 sp905198755	77.9788	89	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553225.1	s__CAG-492 sp900553225	77.756	107	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	98.27	97.59	0.83	0.79	3	-
GCA_904419495.1	s__CAG-269 sp904419495	77.7106	122	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714565.1	s__Merdicola faecigallinarum	77.6191	128	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	99.96	99.96	0.95	0.95	2	-
GCA_900759475.1	s__UMGS1754 sp900759475	77.6113	114	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1754	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434015.1	s__CAG-492 sp000434015	77.5785	127	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
GCA_905215845.1	s__CAG-269 sp905215845	77.5208	76	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513065.1	s__UMGS1663 sp012513065	77.4732	111	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435755.1	s__CAG-273 sp000435755	77.4598	79	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.67	98.38	0.92	0.88	3	-
GCA_900556695.1	s__CAG-269 sp900556695	77.3189	89	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420285.1	s__CAG-273 sp904420285	77.1913	92	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904384245.1	s__CAG-269 sp904384245	77.1755	129	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215615.1	s__CAG-273 sp905215615	77.1674	59	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759015.1	s__Merdicola sp900759015	77.1527	98	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772235.1	s__UMGS1933 sp900772235	76.7558	81	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1933	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397545.1	s__CAG-452 sp017397545	76.6418	100	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469445.1	s__UMGS1864 sp017469445	76.5975	79	377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1864	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:00:17,800] [INFO] GTDB search result was written to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:00:17,801] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:00:17,804] [INFO] DFAST_QC result json was written to GCA_947573985.1_SRR15730551_bin.78_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:00:17,804] [INFO] DFAST_QC completed!
[2023-06-08 12:00:17,804] [INFO] Total running time: 0h0m35s