[2023-06-13 22:21:34,981] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:21:34,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:21:34,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference
[2023-06-13 22:21:36,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:21:36,208] [INFO] Task started: Prodigal
[2023-06-13 22:21:36,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg88de292a-9b10-4319-8155-4276b67126a4/GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:21:39,012] [INFO] Task succeeded: Prodigal
[2023-06-13 22:21:39,012] [INFO] Task started: HMMsearch
[2023-06-13 22:21:39,012] [INFO] Running command: hmmsearch --tblout GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/reference_markers.hmm GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:21:39,257] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:21:39,259] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88de292a-9b10-4319-8155-4276b67126a4/GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 22:21:39,281] [INFO] Query marker FASTA was written to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 22:21:39,281] [INFO] Task started: Blastn
[2023-06-13 22:21:39,281] [INFO] Running command: blastn -query GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/reference_markers.fasta -out GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:21:40,172] [INFO] Task succeeded: Blastn
[2023-06-13 22:21:40,177] [INFO] Selected 20 target genomes.
[2023-06-13 22:21:40,178] [INFO] Target genome list was writen to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 22:21:40,180] [INFO] Task started: fastANI
[2023-06-13 22:21:40,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg88de292a-9b10-4319-8155-4276b67126a4/GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:21:48,990] [INFO] Task succeeded: fastANI
[2023-06-13 22:21:48,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:21:48,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:21:49,000] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:21:49,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:21:49,000] [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
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	75.1522	50	529	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.9521	55	529	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	74.9224	52	529	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	74.7592	50	529	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:21:49,003] [INFO] DFAST Taxonomy check result was written to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 22:21:49,003] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:21:49,003] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:21:49,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/checkm_data
[2023-06-13 22:21:49,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:21:49,030] [INFO] Task started: CheckM
[2023-06-13 22:21:49,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 22:22:05,624] [INFO] Task succeeded: CheckM
[2023-06-13 22:22:05,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:22:05,648] [INFO] ===== Completeness check finished =====
[2023-06-13 22:22:05,649] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:22:05,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 22:22:05,650] [INFO] Task started: Blastn
[2023-06-13 22:22:05,650] [INFO] Running command: blastn -query GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg201de8ab-c0f5-4e0c-ab35-f5212e706bb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:22:06,462] [INFO] Task succeeded: Blastn
[2023-06-13 22:22:06,468] [INFO] Selected 18 target genomes.
[2023-06-13 22:22:06,468] [INFO] Target genome list was writen to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:22:06,470] [INFO] Task started: fastANI
[2023-06-13 22:22:06,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg88de292a-9b10-4319-8155-4276b67126a4/GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:22:11,136] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:11,158] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:22:11,158] [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_904381285.1	s__RGIG8482 sp904381285	81.0283	290	529	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_017626365.1	s__RGIG8482 sp017626365	80.9284	269	529	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	78.6513	115	529	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_905215845.1	s__CAG-269 sp905215845	78.4201	97	529	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_900556695.1	s__CAG-269 sp900556695	78.3958	98	529	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_900553405.1	s__UMGS1663 sp900553405	78.1892	156	529	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_900553985.1	s__CAG-269 sp900553985	78.1162	152	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
GCA_017397545.1	s__CAG-452 sp017397545	78.0475	124	529	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_900770385.1	s__HGM13634 sp900770385	78.0391	130	529	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_017434295.1	s__CAG-269 sp017434295	77.9412	110	529	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_000434035.1	s__CAG-452 sp000434035	77.8421	141	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	98.46	98.21	0.89	0.89	3	-
GCA_904419495.1	s__CAG-269 sp904419495	77.7972	128	529	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_900770415.1	s__CAG-452 sp900770415	77.6982	124	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	97.84	97.84	0.80	0.80	2	-
GCA_018714565.1	s__Merdicola faecigallinarum	77.5611	129	529	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_900555835.1	s__UMGS1864 sp900555835	77.5304	108	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1864	95.0	99.90	99.90	0.84	0.84	2	-
GCA_017475185.1	s__CAG-492 sp017475185	77.4326	116	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438255.1	s__CAG-269 sp000438255	77.1849	130	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_900553695.1	s__UMGS1781 sp900553695	76.9165	84	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781	95.0	98.77	98.67	0.87	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-13 22:22:11,160] [INFO] GTDB search result was written to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 22:22:11,161] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:22:11,167] [INFO] DFAST_QC result json was written to GCA_947644945.1_SRR19759413_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 22:22:11,167] [INFO] DFAST_QC completed!
[2023-06-13 22:22:11,167] [INFO] Total running time: 0h0m36s