[2023-06-05 18:56:56,566] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:56,568] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:56,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference
[2023-06-05 18:56:58,054] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:58,055] [INFO] Task started: Prodigal
[2023-06-05 18:56:58,055] [INFO] Running command: gunzip -c /var/lib/cwl/stg39a079ee-fbf4-45e8-b836-5c2379e1d2e3/GCA_934446375.1_ERR7738447_bin.60_genomic.fna.gz | prodigal -d GCA_934446375.1_ERR7738447_bin.60_genomic.fna/cds.fna -a GCA_934446375.1_ERR7738447_bin.60_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:01,685] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:01,685] [INFO] Task started: HMMsearch
[2023-06-05 18:57:01,685] [INFO] Running command: hmmsearch --tblout GCA_934446375.1_ERR7738447_bin.60_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/reference_markers.hmm GCA_934446375.1_ERR7738447_bin.60_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:01,936] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:01,937] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39a079ee-fbf4-45e8-b836-5c2379e1d2e3/GCA_934446375.1_ERR7738447_bin.60_genomic.fna.gz]
[2023-06-05 18:57:01,966] [INFO] Query marker FASTA was written to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/markers.fasta
[2023-06-05 18:57:01,966] [INFO] Task started: Blastn
[2023-06-05 18:57:01,967] [INFO] Running command: blastn -query GCA_934446375.1_ERR7738447_bin.60_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/reference_markers.fasta -out GCA_934446375.1_ERR7738447_bin.60_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:02,618] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:02,622] [INFO] Selected 18 target genomes.
[2023-06-05 18:57:02,623] [INFO] Target genome list was writen to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/target_genomes.txt
[2023-06-05 18:57:02,631] [INFO] Task started: fastANI
[2023-06-05 18:57:02,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg39a079ee-fbf4-45e8-b836-5c2379e1d2e3/GCA_934446375.1_ERR7738447_bin.60_genomic.fna.gz --refList GCA_934446375.1_ERR7738447_bin.60_genomic.fna/target_genomes.txt --output GCA_934446375.1_ERR7738447_bin.60_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:13,493] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:13,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:13,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:13,496] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:13,497] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:57:13,497] [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
--------------------------------------------------------------------------------
[2023-06-05 18:57:13,502] [INFO] DFAST Taxonomy check result was written to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/tc_result.tsv
[2023-06-05 18:57:13,502] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:13,503] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:13,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/checkm_data
[2023-06-05 18:57:13,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:13,535] [INFO] Task started: CheckM
[2023-06-05 18:57:13,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934446375.1_ERR7738447_bin.60_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934446375.1_ERR7738447_bin.60_genomic.fna/checkm_input GCA_934446375.1_ERR7738447_bin.60_genomic.fna/checkm_result
[2023-06-05 18:57:32,406] [INFO] Task succeeded: CheckM
[2023-06-05 18:57:32,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:57:32,439] [INFO] ===== Completeness check finished =====
[2023-06-05 18:57:32,439] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:57:32,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934446375.1_ERR7738447_bin.60_genomic.fna/markers.fasta)
[2023-06-05 18:57:32,440] [INFO] Task started: Blastn
[2023-06-05 18:57:32,440] [INFO] Running command: blastn -query GCA_934446375.1_ERR7738447_bin.60_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f3a0cb-dbfd-4074-a400-cb86e39154e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934446375.1_ERR7738447_bin.60_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:33,377] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:33,381] [INFO] Selected 23 target genomes.
[2023-06-05 18:57:33,381] [INFO] Target genome list was writen to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:57:33,388] [INFO] Task started: fastANI
[2023-06-05 18:57:33,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg39a079ee-fbf4-45e8-b836-5c2379e1d2e3/GCA_934446375.1_ERR7738447_bin.60_genomic.fna.gz --refList GCA_934446375.1_ERR7738447_bin.60_genomic.fna/target_genomes_gtdb.txt --output GCA_934446375.1_ERR7738447_bin.60_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:57:39,882] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:39,895] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:57:39,896] [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_900549755.1	s__UBA737 sp900549755	78.5519	113	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.98	97.93	0.82	0.76	3	-
GCA_905193585.1	s__UBA737 sp905193585	78.4807	105	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547305.1	s__UBA737 sp900547305	78.4747	114	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.91	99.91	0.93	0.93	2	-
GCA_900549055.1	s__UBA737 sp900549055	78.1722	101	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.22	96.30	0.81	0.81	4	-
GCA_002431945.1	s__UBA737 sp002431945	78.1666	133	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.08	96.44	0.77	0.66	6	-
GCA_902762875.1	s__UBA737 sp902762875	77.8926	101	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.81	98.63	0.89	0.87	3	-
GCA_900547445.1	s__UBA737 sp900547445	77.8697	116	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.98	99.98	0.91	0.91	2	-
GCA_900754145.1	s__UBA737 sp900754145	77.8656	78	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.37	97.01	0.81	0.78	3	-
GCA_904501875.1	s__UBA737 sp904501875	77.823	80	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900543215.1	s__UBA737 sp900543215	77.7815	117	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.02	96.96	0.84	0.79	3	-
GCA_017472575.1	s__UBA737 sp017472575	77.7759	81	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451855.1	s__UBA737 sp002451855	77.4898	116	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303035.1	s__UBA737 sp016303035	77.2808	107	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507805.1	s__UBA737 sp017507805	77.247	65	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302625.1	s__UBA737 sp016302625	77.1619	74	514	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:57:39,898] [INFO] GTDB search result was written to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/result_gtdb.tsv
[2023-06-05 18:57:39,899] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:57:39,904] [INFO] DFAST_QC result json was written to GCA_934446375.1_ERR7738447_bin.60_genomic.fna/dqc_result.json
[2023-06-05 18:57:39,904] [INFO] DFAST_QC completed!
[2023-06-05 18:57:39,904] [INFO] Total running time: 0h0m43s