[2023-06-29 13:03:07,790] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:03:07,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:03:07,793] [INFO] DQC Reference Directory: /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference
[2023-06-29 13:03:08,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:03:08,993] [INFO] Task started: Prodigal
[2023-06-29 13:03:08,994] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5369c8e-5e7c-41b7-b6ca-2a0ebc67742b/GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:03:12,726] [INFO] Task succeeded: Prodigal
[2023-06-29 13:03:12,727] [INFO] Task started: HMMsearch
[2023-06-29 13:03:12,727] [INFO] Running command: hmmsearch --tblout GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/reference_markers.hmm GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:03:12,965] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:03:12,966] [INFO] Found 6/6 markers.
[2023-06-29 13:03:12,993] [INFO] Query marker FASTA was written to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:03:12,994] [INFO] Task started: Blastn
[2023-06-29 13:03:12,994] [INFO] Running command: blastn -query GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/reference_markers.fasta -out GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:03:13,610] [INFO] Task succeeded: Blastn
[2023-06-29 13:03:13,616] [INFO] Selected 15 target genomes.
[2023-06-29 13:03:13,616] [INFO] Target genome list was writen to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:03:13,644] [INFO] Task started: fastANI
[2023-06-29 13:03:13,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5369c8e-5e7c-41b7-b6ca-2a0ebc67742b/GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:03:22,901] [INFO] Task succeeded: fastANI
[2023-06-29 13:03:22,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:03:22,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:03:22,904] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:03:22,904] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:03:22,904] [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
--------------------------------------------------------------------------------
[2023-06-29 13:03:22,906] [INFO] DFAST Taxonomy check result was written to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:03:22,906] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:03:22,907] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:03:22,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/checkm_data
[2023-06-29 13:03:22,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:03:22,936] [INFO] Task started: CheckM
[2023-06-29 13:03:22,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:03:42,698] [INFO] Task succeeded: CheckM
[2023-06-29 13:03:42,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 13:03:42,733] [INFO] ===== Completeness check finished =====
[2023-06-29 13:03:42,734] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:03:42,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:03:42,735] [INFO] Task started: Blastn
[2023-06-29 13:03:42,735] [INFO] Running command: blastn -query GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f37a5b-5f91-4b90-a8e7-e2b36bbdea71/dqc_reference/reference_markers_gtdb.fasta -out GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:03:43,747] [INFO] Task succeeded: Blastn
[2023-06-29 13:03:43,751] [INFO] Selected 22 target genomes.
[2023-06-29 13:03:43,752] [INFO] Target genome list was writen to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:03:43,801] [INFO] Task started: fastANI
[2023-06-29 13:03:43,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5369c8e-5e7c-41b7-b6ca-2a0ebc67742b/GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:03:54,528] [INFO] Task succeeded: fastANI
[2023-06-29 13:03:54,538] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:03:54,539] [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_003477045.1	s__UBA12480 sp003477045	87.1393	393	497	d__Bacteria;p__Delongbacteria;c__UBA4055;o__UBA4055;f__UBA4055;g__UBA12480	95.0	99.62	99.62	0.91	0.91	2	-
GCA_002382735.1	s__UBA4055 sp002382735	77.4048	90	497	d__Bacteria;p__Delongbacteria;c__UBA4055;o__UBA4055;f__UBA4055;g__UBA4055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252515.1	s__UBA4055 sp003252515	76.7255	88	497	d__Bacteria;p__Delongbacteria;c__UBA4055;o__UBA4055;f__UBA4055;g__UBA4055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938535.1	s__SLFX01 sp016938535	76.649	55	497	d__Bacteria;p__Delongbacteria;c__UBA4055;o__UBA4055;f__UBA4055;g__SLFX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:03:54,541] [INFO] GTDB search result was written to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:03:54,542] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:03:54,545] [INFO] DFAST_QC result json was written to GCA_937873545.1_SRR8868559_bin.84_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:03:54,545] [INFO] DFAST_QC completed!
[2023-06-29 13:03:54,546] [INFO] Total running time: 0h0m47s