[2023-06-29 16:29:57,636] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:29:57,641] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:29:57,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference
[2023-06-29 16:29:58,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:29:58,823] [INFO] Task started: Prodigal
[2023-06-29 16:29:58,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg74aa355e-a75b-4e85-b044-e0261e66977c/GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:30:00,656] [INFO] Task succeeded: Prodigal
[2023-06-29 16:30:00,656] [INFO] Task started: HMMsearch
[2023-06-29 16:30:00,657] [INFO] Running command: hmmsearch --tblout GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/reference_markers.hmm GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:30:00,886] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:30:00,888] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg74aa355e-a75b-4e85-b044-e0261e66977c/GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 16:30:00,914] [INFO] Query marker FASTA was written to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:30:00,914] [INFO] Task started: Blastn
[2023-06-29 16:30:00,914] [INFO] Running command: blastn -query GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/reference_markers.fasta -out GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:01,615] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:01,620] [INFO] Selected 24 target genomes.
[2023-06-29 16:30:01,621] [INFO] Target genome list was writen to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:30:01,633] [INFO] Task started: fastANI
[2023-06-29 16:30:01,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg74aa355e-a75b-4e85-b044-e0261e66977c/GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:30:12,232] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:12,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:30:12,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:30:12,234] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:30:12,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:30:12,235] [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 16:30:12,237] [INFO] DFAST Taxonomy check result was written to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:30:12,237] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:30:12,238] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:30:12,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/checkm_data
[2023-06-29 16:30:12,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:30:12,260] [INFO] Task started: CheckM
[2023-06-29 16:30:12,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:30:26,811] [INFO] Task succeeded: CheckM
[2023-06-29 16:30:26,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:30:26,835] [INFO] ===== Completeness check finished =====
[2023-06-29 16:30:26,836] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:30:26,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:30:26,837] [INFO] Task started: Blastn
[2023-06-29 16:30:26,837] [INFO] Running command: blastn -query GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cd86a25-e59f-4146-ab52-f074aa746586/dqc_reference/reference_markers_gtdb.fasta -out GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:27,853] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:27,858] [INFO] Selected 16 target genomes.
[2023-06-29 16:30:27,858] [INFO] Target genome list was writen to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:30:27,869] [INFO] Task started: fastANI
[2023-06-29 16:30:27,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg74aa355e-a75b-4e85-b044-e0261e66977c/GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:30:32,444] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:32,448] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:30:32,448] [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_012839485.1	s__DUNF01 sp012839485	96.2282	215	375	d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__DUNF01	95.0	95.61	95.61	0.71	0.71	2	conclusive
GCA_012838635.1	s__DUNF01 sp012838635	85.9877	254	375	d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__DUNF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:30:32,450] [INFO] GTDB search result was written to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:30:32,451] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:30:32,455] [INFO] DFAST_QC result json was written to GCA_937863855.1_ERR2113684_bin.63_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:30:32,455] [INFO] DFAST_QC completed!
[2023-06-29 16:30:32,455] [INFO] Total running time: 0h0m35s