[2023-06-07 19:37:21,358] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:37:21,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:37:21,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference
[2023-06-07 19:37:22,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:37:22,720] [INFO] Task started: Prodigal
[2023-06-07 19:37:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bc271e1-0eab-49ae-87de-17fb699c7674/GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:37:24,269] [INFO] Task succeeded: Prodigal
[2023-06-07 19:37:24,269] [INFO] Task started: HMMsearch
[2023-06-07 19:37:24,270] [INFO] Running command: hmmsearch --tblout GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/reference_markers.hmm GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:37:24,495] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:37:24,496] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2bc271e1-0eab-49ae-87de-17fb699c7674/GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-07 19:37:24,514] [INFO] Query marker FASTA was written to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-07 19:37:24,514] [INFO] Task started: Blastn
[2023-06-07 19:37:24,514] [INFO] Running command: blastn -query GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/reference_markers.fasta -out GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:37:25,161] [INFO] Task succeeded: Blastn
[2023-06-07 19:37:25,168] [INFO] Selected 17 target genomes.
[2023-06-07 19:37:25,168] [INFO] Target genome list was writen to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-07 19:37:25,170] [INFO] Task started: fastANI
[2023-06-07 19:37:25,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bc271e1-0eab-49ae-87de-17fb699c7674/GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:37:31,318] [INFO] Task succeeded: fastANI
[2023-06-07 19:37:31,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:37:31,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:37:31,322] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:37:31,322] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:37:31,322] [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
--------------------------------------------------------------------------------
[2023-06-07 19:37:31,324] [INFO] DFAST Taxonomy check result was written to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-07 19:37:31,324] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:37:31,325] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:37:31,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/checkm_data
[2023-06-07 19:37:31,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:37:31,349] [INFO] Task started: CheckM
[2023-06-07 19:37:31,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-07 19:37:45,612] [INFO] Task succeeded: CheckM
[2023-06-07 19:37:45,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 19:37:45,632] [INFO] ===== Completeness check finished =====
[2023-06-07 19:37:45,633] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:37:45,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-07 19:37:45,633] [INFO] Task started: Blastn
[2023-06-07 19:37:45,633] [INFO] Running command: blastn -query GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg377858b9-d7a0-4b06-868c-2d00b7a276c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:37:46,376] [INFO] Task succeeded: Blastn
[2023-06-07 19:37:46,381] [INFO] Selected 18 target genomes.
[2023-06-07 19:37:46,381] [INFO] Target genome list was writen to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:37:46,388] [INFO] Task started: fastANI
[2023-06-07 19:37:46,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bc271e1-0eab-49ae-87de-17fb699c7674/GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:37:50,077] [INFO] Task succeeded: fastANI
[2023-06-07 19:37:50,082] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:37:50,083] [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_018713045.1	s__Coprosoma intestinipullorum	97.8323	238	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	97.64	97.54	0.77	0.76	4	conclusive
GCA_000432855.1	s__Coprosoma sp000432855	78.449	81	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783895.1	s__Coprosoma sp902783895	77.4672	90	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	98.50	98.50	0.95	0.95	2	-
GCA_017513865.1	s__Coprosoma sp017513865	77.1297	54	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318075.1	s__Coprosoma sp900318075	76.7258	59	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	99.91	99.91	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-07 19:37:50,085] [INFO] GTDB search result was written to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 19:37:50,086] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:37:50,089] [INFO] DFAST_QC result json was written to GCA_927360075.1_SRR789046_bin.11_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-07 19:37:50,089] [INFO] DFAST_QC completed!
[2023-06-07 19:37:50,090] [INFO] Total running time: 0h0m29s