[2023-06-19 08:45:31,828] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:31,830] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:31,830] [INFO] DQC Reference Directory: /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference
[2023-06-19 08:45:35,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:35,359] [INFO] Task started: Prodigal
[2023-06-19 08:45:35,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgce5fcdf2-6f17-4aa4-a553-69023d022c81/GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:37,815] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:37,815] [INFO] Task started: HMMsearch
[2023-06-19 08:45:37,816] [INFO] Running command: hmmsearch --tblout GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/reference_markers.hmm GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:38,090] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:38,091] [INFO] Found 6/6 markers.
[2023-06-19 08:45:38,112] [INFO] Query marker FASTA was written to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 08:45:38,113] [INFO] Task started: Blastn
[2023-06-19 08:45:38,113] [INFO] Running command: blastn -query GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/reference_markers.fasta -out GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:40,746] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:40,752] [INFO] Selected 10 target genomes.
[2023-06-19 08:45:40,753] [INFO] Target genome list was writen to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 08:45:40,757] [INFO] Task started: fastANI
[2023-06-19 08:45:40,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgce5fcdf2-6f17-4aa4-a553-69023d022c81/GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:45:46,763] [INFO] Task succeeded: fastANI
[2023-06-19 08:45:46,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:45:46,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:45:46,767] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:45:46,767] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:45:46,767] [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
--------------------------------------------------------------------------------
[2023-06-19 08:45:46,770] [INFO] DFAST Taxonomy check result was written to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 08:45:46,772] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:45:46,772] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:45:46,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/checkm_data
[2023-06-19 08:45:46,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:45:46,794] [INFO] Task started: CheckM
[2023-06-19 08:45:46,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 08:46:02,181] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:02,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:02,226] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:02,227] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:02,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 08:46:02,228] [INFO] Task started: Blastn
[2023-06-19 08:46:02,228] [INFO] Running command: blastn -query GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgce21165c-16a4-4a00-a83e-98b87d6c83b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:03,091] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:03,095] [INFO] Selected 17 target genomes.
[2023-06-19 08:46:03,095] [INFO] Target genome list was writen to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:03,106] [INFO] Task started: fastANI
[2023-06-19 08:46:03,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgce5fcdf2-6f17-4aa4-a553-69023d022c81/GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:06,346] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:06,356] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:46:06,356] [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_002371895.1	s__UBA2834 sp002371895	79.2932	128	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437945.1	s__UBA2834 sp017437945	79.0578	105	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964115.1	s__UBA2834 sp017964115	78.8316	83	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002351365.1	s__UBA2834 sp002351365	78.8204	99	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524405.1	s__UBA2834 sp017524405	78.4558	78	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	97.50	97.50	0.94	0.94	2	-
GCA_002363515.1	s__UBA2834 sp002363515	78.4314	73	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	97.02	97.02	0.88	0.88	2	-
GCA_016290315.1	s__UBA2834 sp016290315	78.4223	96	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540545.1	s__UBA2834 sp017540545	77.9233	80	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361425.1	s__UBA2834 sp002361425	77.5154	77	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017514805.1	s__UBA2834 sp017514805	77.4299	74	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391075.1	s__UBA2834 sp002391075	76.6957	56	316	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:06,359] [INFO] GTDB search result was written to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:06,359] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:06,362] [INFO] DFAST_QC result json was written to GCA_937906385.1_ERR1278103_bin.189_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 08:46:06,363] [INFO] DFAST_QC completed!
[2023-06-19 08:46:06,363] [INFO] Total running time: 0h0m35s