[2023-06-05 02:27:08,535] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:27:08,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:27:08,542] [INFO] DQC Reference Directory: /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference
[2023-06-05 02:27:09,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:27:09,969] [INFO] Task started: Prodigal
[2023-06-05 02:27:09,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba2138f-27bf-485a-87ef-b5ac848151fe/GCA_934101355.1_ERR7738560_bin.56_genomic.fna.gz | prodigal -d GCA_934101355.1_ERR7738560_bin.56_genomic.fna/cds.fna -a GCA_934101355.1_ERR7738560_bin.56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:27:11,791] [INFO] Task succeeded: Prodigal
[2023-06-05 02:27:11,792] [INFO] Task started: HMMsearch
[2023-06-05 02:27:11,792] [INFO] Running command: hmmsearch --tblout GCA_934101355.1_ERR7738560_bin.56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/reference_markers.hmm GCA_934101355.1_ERR7738560_bin.56_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:27:12,024] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:27:12,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdba2138f-27bf-485a-87ef-b5ac848151fe/GCA_934101355.1_ERR7738560_bin.56_genomic.fna.gz]
[2023-06-05 02:27:12,040] [INFO] Query marker FASTA was written to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/markers.fasta
[2023-06-05 02:27:12,041] [INFO] Task started: Blastn
[2023-06-05 02:27:12,041] [INFO] Running command: blastn -query GCA_934101355.1_ERR7738560_bin.56_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/reference_markers.fasta -out GCA_934101355.1_ERR7738560_bin.56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:12,655] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:12,659] [INFO] Selected 30 target genomes.
[2023-06-05 02:27:12,660] [INFO] Target genome list was writen to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/target_genomes.txt
[2023-06-05 02:27:12,665] [INFO] Task started: fastANI
[2023-06-05 02:27:12,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba2138f-27bf-485a-87ef-b5ac848151fe/GCA_934101355.1_ERR7738560_bin.56_genomic.fna.gz --refList GCA_934101355.1_ERR7738560_bin.56_genomic.fna/target_genomes.txt --output GCA_934101355.1_ERR7738560_bin.56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:27:25,034] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:25,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:27:25,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:27:25,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:27:25,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:27:25,038] [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 02:27:25,041] [INFO] DFAST Taxonomy check result was written to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/tc_result.tsv
[2023-06-05 02:27:25,041] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:27:25,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:27:25,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/checkm_data
[2023-06-05 02:27:25,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:27:25,061] [INFO] Task started: CheckM
[2023-06-05 02:27:25,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934101355.1_ERR7738560_bin.56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934101355.1_ERR7738560_bin.56_genomic.fna/checkm_input GCA_934101355.1_ERR7738560_bin.56_genomic.fna/checkm_result
[2023-06-05 02:27:39,365] [INFO] Task succeeded: CheckM
[2023-06-05 02:27:39,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:27:39,386] [INFO] ===== Completeness check finished =====
[2023-06-05 02:27:39,386] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:27:39,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934101355.1_ERR7738560_bin.56_genomic.fna/markers.fasta)
[2023-06-05 02:27:39,387] [INFO] Task started: Blastn
[2023-06-05 02:27:39,387] [INFO] Running command: blastn -query GCA_934101355.1_ERR7738560_bin.56_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c4d198-1693-4a2b-a7a7-26486a5fa121/dqc_reference/reference_markers_gtdb.fasta -out GCA_934101355.1_ERR7738560_bin.56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:40,199] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:40,203] [INFO] Selected 17 target genomes.
[2023-06-05 02:27:40,204] [INFO] Target genome list was writen to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:27:40,207] [INFO] Task started: fastANI
[2023-06-05 02:27:40,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba2138f-27bf-485a-87ef-b5ac848151fe/GCA_934101355.1_ERR7738560_bin.56_genomic.fna.gz --refList GCA_934101355.1_ERR7738560_bin.56_genomic.fna/target_genomes_gtdb.txt --output GCA_934101355.1_ERR7738560_bin.56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:27:43,895] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:43,904] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:27:43,904] [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_900543825.1	s__CAG-302 sp900543825	97.8771	319	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.18	98.11	0.88	0.87	3	conclusive
GCA_001916775.1	s__CAG-302 sp001916775	81.8876	215	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	95.82	95.12	0.84	0.77	8	-
GCA_000431795.1	s__CAG-302 sp000431795	81.0826	199	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.56	98.47	0.90	0.88	5	-
GCA_900548425.1	s__CAG-302 sp900548425	80.8212	194	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	99.47	98.99	0.91	0.87	3	-
GCA_900554615.1	s__CAG-302 sp900554615	80.706	162	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.40	97.12	0.84	0.78	3	-
GCA_900549325.1	s__CAG-302 sp900549325	80.6032	183	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	97.65	95.34	0.85	0.78	3	-
GCA_002375205.1	s__CAG-302 sp002375205	79.3913	137	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	97.06	96.95	0.78	0.76	3	-
GCA_900759875.1	s__RUG705 sp900759875	78.1698	52	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG705	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017887885.1	s__CAG-302 sp017887885	77.9061	105	363	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:27:43,906] [INFO] GTDB search result was written to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/result_gtdb.tsv
[2023-06-05 02:27:43,907] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:27:43,911] [INFO] DFAST_QC result json was written to GCA_934101355.1_ERR7738560_bin.56_genomic.fna/dqc_result.json
[2023-06-05 02:27:43,912] [INFO] DFAST_QC completed!
[2023-06-05 02:27:43,912] [INFO] Total running time: 0h0m35s