[2023-06-08 14:28:14,988] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:14,997] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:14,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference
[2023-06-08 14:28:18,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:18,272] [INFO] Task started: Prodigal
[2023-06-08 14:28:18,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgf75c02a3-5bc8-46be-9b35-459da2bd5079/GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:22,777] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:22,778] [INFO] Task started: HMMsearch
[2023-06-08 14:28:22,778] [INFO] Running command: hmmsearch --tblout GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/reference_markers.hmm GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:23,143] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:23,145] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf75c02a3-5bc8-46be-9b35-459da2bd5079/GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 14:28:23,190] [INFO] Query marker FASTA was written to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:28:23,190] [INFO] Task started: Blastn
[2023-06-08 14:28:23,190] [INFO] Running command: blastn -query GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/reference_markers.fasta -out GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:24,392] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:24,396] [INFO] Selected 16 target genomes.
[2023-06-08 14:28:24,396] [INFO] Target genome list was writen to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:28:24,400] [INFO] Task started: fastANI
[2023-06-08 14:28:24,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75c02a3-5bc8-46be-9b35-459da2bd5079/GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:35,705] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:35,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:35,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:35,707] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:35,708] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:28:35,708] [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 14:28:35,710] [INFO] DFAST Taxonomy check result was written to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:28:35,711] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:35,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:35,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/checkm_data
[2023-06-08 14:28:35,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:35,740] [INFO] Task started: CheckM
[2023-06-08 14:28:35,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:28:56,608] [INFO] Task succeeded: CheckM
[2023-06-08 14:28:56,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:28:56,631] [INFO] ===== Completeness check finished =====
[2023-06-08 14:28:56,632] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:28:56,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:28:56,632] [INFO] Task started: Blastn
[2023-06-08 14:28:56,633] [INFO] Running command: blastn -query GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg302a3b6f-4436-4c6c-b174-318e430bd7a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:57,412] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:57,419] [INFO] Selected 17 target genomes.
[2023-06-08 14:28:57,420] [INFO] Target genome list was writen to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:28:57,433] [INFO] Task started: fastANI
[2023-06-08 14:28:57,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75c02a3-5bc8-46be-9b35-459da2bd5079/GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:04,118] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:04,134] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:29:04,134] [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_900317165.1	s__Enteromonas sp900317165	94.5145	425	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	98.79	97.70	0.92	0.82	4	-
GCA_017454295.1	s__Enteromonas sp017454295	79.362	56	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017445245.1	s__Enteromonas sp017445245	79.1937	58	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058945.1	s__Enteromonas sp015058945	78.9739	81	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450325.1	s__Enteromonas sp017450325	78.8242	74	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317295.1	s__Enteromonas sp900317295	78.5579	81	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	97.85	96.56	0.86	0.84	3	-
GCA_002472275.1	s__Enteromonas sp002472275	78.3721	63	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	95.44	95.44	0.87	0.87	2	-
GCA_902773005.1	s__Enteromonas sp902773005	78.0258	66	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	96.49	96.49	0.77	0.77	2	-
GCA_017626815.1	s__Enteromonas sp017626815	77.8144	75	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	98.43	98.43	0.85	0.85	2	-
GCA_902803375.1	s__Enteromonas sp902803375	77.2876	68	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Enteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:04,136] [INFO] GTDB search result was written to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:04,137] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:04,139] [INFO] DFAST_QC result json was written to GCA_947166565.1_SRR8387716_bin.60_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:29:04,139] [INFO] DFAST_QC completed!
[2023-06-08 14:29:04,140] [INFO] Total running time: 0h0m49s