[2023-07-01 02:42:37,045] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:42:37,053] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:42:37,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference
[2023-07-01 02:42:38,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:42:38,379] [INFO] Task started: Prodigal
[2023-07-01 02:42:38,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg980ab727-4b77-4e27-9396-25b93995a02d/GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna.gz | prodigal -d GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/cds.fna -a GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:42:44,024] [INFO] Task succeeded: Prodigal
[2023-07-01 02:42:44,024] [INFO] Task started: HMMsearch
[2023-07-01 02:42:44,025] [INFO] Running command: hmmsearch --tblout GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/reference_markers.hmm GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:42:44,248] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:42:44,249] [INFO] Found 6/6 markers.
[2023-07-01 02:42:44,279] [INFO] Query marker FASTA was written to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/markers.fasta
[2023-07-01 02:42:44,280] [INFO] Task started: Blastn
[2023-07-01 02:42:44,280] [INFO] Running command: blastn -query GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/markers.fasta -db /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/reference_markers.fasta -out GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:42:44,883] [INFO] Task succeeded: Blastn
[2023-07-01 02:42:44,887] [INFO] Selected 8 target genomes.
[2023-07-01 02:42:44,887] [INFO] Target genome list was writen to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/target_genomes.txt
[2023-07-01 02:42:44,888] [INFO] Task started: fastANI
[2023-07-01 02:42:44,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg980ab727-4b77-4e27-9396-25b93995a02d/GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna.gz --refList GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/target_genomes.txt --output GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:42:51,235] [INFO] Task succeeded: fastANI
[2023-07-01 02:42:51,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:42:51,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:42:51,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:42:51,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 02:42:51,239] [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
--------------------------------------------------------------------------------
[2023-07-01 02:42:51,240] [INFO] DFAST Taxonomy check result was written to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/tc_result.tsv
[2023-07-01 02:42:51,241] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:42:51,241] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:42:51,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/checkm_data
[2023-07-01 02:42:51,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:42:51,270] [INFO] Task started: CheckM
[2023-07-01 02:42:51,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/checkm_input GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/checkm_result
[2023-07-01 02:43:15,201] [INFO] Task succeeded: CheckM
[2023-07-01 02:43:15,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-07-01 02:43:15,221] [INFO] ===== Completeness check finished =====
[2023-07-01 02:43:15,222] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:43:15,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/markers.fasta)
[2023-07-01 02:43:15,222] [INFO] Task started: Blastn
[2023-07-01 02:43:15,222] [INFO] Running command: blastn -query GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/markers.fasta -db /var/lib/cwl/stg96836aa9-48ac-45fa-8f04-ca920b2d5f97/dqc_reference/reference_markers_gtdb.fasta -out GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:43:16,080] [INFO] Task succeeded: Blastn
[2023-07-01 02:43:16,085] [INFO] Selected 6 target genomes.
[2023-07-01 02:43:16,085] [INFO] Target genome list was writen to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:43:16,086] [INFO] Task started: fastANI
[2023-07-01 02:43:16,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg980ab727-4b77-4e27-9396-25b93995a02d/GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna.gz --refList GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/target_genomes_gtdb.txt --output GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:43:18,792] [INFO] Task succeeded: fastANI
[2023-07-01 02:43:18,798] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:43:18,798] [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_903871855.1	s__Cryosericum sp903871855	99.9859	565	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	99.97	99.88	0.97	0.92	8	conclusive
GCF_003570995.1	s__Cryosericum septentrionale	85.8025	412	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570925.1	s__Cryosericum terrychapinii	85.7375	336	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013824685.1	s__Cryosericum sp013824685	85.37	418	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570985.1	s__Cryosericum hinesii	84.7915	414	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	99.90	99.82	0.96	0.94	6	-
GCF_003570935.1	s__Cryosericum odellii	83.9682	332	580	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Cryosericales;f__Cryosericaceae;g__Cryosericum	95.0	99.33	98.95	0.83	0.74	4	-
--------------------------------------------------------------------------------
[2023-07-01 02:43:18,800] [INFO] GTDB search result was written to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/result_gtdb.tsv
[2023-07-01 02:43:18,801] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:43:18,803] [INFO] DFAST_QC result json was written to GCA_903829005.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0503_genomic.fna/dqc_result.json
[2023-07-01 02:43:18,804] [INFO] DFAST_QC completed!
[2023-07-01 02:43:18,804] [INFO] Total running time: 0h0m42s