[2023-06-08 13:03:21,946] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:03:21,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:03:21,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference
[2023-06-08 13:03:23,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:03:23,776] [INFO] Task started: Prodigal
[2023-06-08 13:03:23,776] [INFO] Running command: gunzip -c /var/lib/cwl/stge692f23b-f313-409f-89c0-ea3466ca5bb3/GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:03:26,393] [INFO] Task succeeded: Prodigal
[2023-06-08 13:03:26,394] [INFO] Task started: HMMsearch
[2023-06-08 13:03:26,394] [INFO] Running command: hmmsearch --tblout GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/reference_markers.hmm GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:03:26,620] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:03:26,621] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge692f23b-f313-409f-89c0-ea3466ca5bb3/GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:03:26,644] [INFO] Query marker FASTA was written to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:03:26,646] [INFO] Task started: Blastn
[2023-06-08 13:03:26,646] [INFO] Running command: blastn -query GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/reference_markers.fasta -out GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:03:27,266] [INFO] Task succeeded: Blastn
[2023-06-08 13:03:27,270] [INFO] Selected 18 target genomes.
[2023-06-08 13:03:27,271] [INFO] Target genome list was writen to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:03:27,278] [INFO] Task started: fastANI
[2023-06-08 13:03:27,278] [INFO] Running command: fastANI --query /var/lib/cwl/stge692f23b-f313-409f-89c0-ea3466ca5bb3/GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:03:35,877] [INFO] Task succeeded: fastANI
[2023-06-08 13:03:35,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:03:35,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:03:35,881] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:03:35,881] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:03:35,881] [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 13:03:35,884] [INFO] DFAST Taxonomy check result was written to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:03:35,884] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:03:35,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:03:35,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/checkm_data
[2023-06-08 13:03:35,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:03:35,907] [INFO] Task started: CheckM
[2023-06-08 13:03:35,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:03:53,055] [INFO] Task succeeded: CheckM
[2023-06-08 13:03:53,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 1.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 13:03:53,089] [INFO] ===== Completeness check finished =====
[2023-06-08 13:03:53,090] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:03:53,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:03:53,091] [INFO] Task started: Blastn
[2023-06-08 13:03:53,091] [INFO] Running command: blastn -query GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg21cdc928-f4af-49ec-8657-c64a45a1679b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:03:54,049] [INFO] Task succeeded: Blastn
[2023-06-08 13:03:54,053] [INFO] Selected 16 target genomes.
[2023-06-08 13:03:54,053] [INFO] Target genome list was writen to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:03:54,057] [INFO] Task started: fastANI
[2023-06-08 13:03:54,057] [INFO] Running command: fastANI --query /var/lib/cwl/stge692f23b-f313-409f-89c0-ea3466ca5bb3/GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:03:59,404] [INFO] Task succeeded: fastANI
[2023-06-08 13:03:59,407] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:03:59,407] [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_000435055.1	s__PeH17 sp000435055	98.0204	237	244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.45	98.03	0.92	0.89	15	conclusive
--------------------------------------------------------------------------------
[2023-06-08 13:03:59,409] [INFO] GTDB search result was written to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:03:59,410] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:03:59,412] [INFO] DFAST_QC result json was written to GCA_947003385.1_SRR19721631_bin.11_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:03:59,412] [INFO] DFAST_QC completed!
[2023-06-08 13:03:59,412] [INFO] Total running time: 0h0m37s