[2023-06-30 16:07:32,990] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:07:32,992] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:07:32,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference
[2023-06-30 16:07:34,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:07:34,152] [INFO] Task started: Prodigal
[2023-06-30 16:07:34,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e76b2f2-695c-4b94-b5b6-977fb2d82817/GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna.gz | prodigal -d GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/cds.fna -a GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:07:38,537] [INFO] Task succeeded: Prodigal
[2023-06-30 16:07:38,537] [INFO] Task started: HMMsearch
[2023-06-30 16:07:38,537] [INFO] Running command: hmmsearch --tblout GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/reference_markers.hmm GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:07:38,736] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:07:38,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e76b2f2-695c-4b94-b5b6-977fb2d82817/GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna.gz]
[2023-06-30 16:07:38,761] [INFO] Query marker FASTA was written to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/markers.fasta
[2023-06-30 16:07:38,761] [INFO] Task started: Blastn
[2023-06-30 16:07:38,761] [INFO] Running command: blastn -query GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/reference_markers.fasta -out GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:07:39,311] [INFO] Task succeeded: Blastn
[2023-06-30 16:07:39,314] [INFO] Selected 11 target genomes.
[2023-06-30 16:07:39,314] [INFO] Target genome list was writen to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/target_genomes.txt
[2023-06-30 16:07:39,320] [INFO] Task started: fastANI
[2023-06-30 16:07:39,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e76b2f2-695c-4b94-b5b6-977fb2d82817/GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna.gz --refList GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/target_genomes.txt --output GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:07:48,007] [INFO] Task succeeded: fastANI
[2023-06-30 16:07:48,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:07:48,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:07:48,011] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:07:48,011] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 16:07:48,011] [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
--------------------------------------------------------------------------------
[2023-06-30 16:07:48,013] [INFO] DFAST Taxonomy check result was written to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/tc_result.tsv
[2023-06-30 16:07:48,013] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:07:48,013] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:07:48,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/checkm_data
[2023-06-30 16:07:48,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:07:48,043] [INFO] Task started: CheckM
[2023-06-30 16:07:48,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/checkm_input GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/checkm_result
[2023-06-30 16:08:07,067] [INFO] Task succeeded: CheckM
[2023-06-30 16:08:07,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.86%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 16:08:07,085] [INFO] ===== Completeness check finished =====
[2023-06-30 16:08:07,085] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:08:07,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/markers.fasta)
[2023-06-30 16:08:07,085] [INFO] Task started: Blastn
[2023-06-30 16:08:07,085] [INFO] Running command: blastn -query GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b8eb18-9bb1-47f9-9f0b-7c249112babb/dqc_reference/reference_markers_gtdb.fasta -out GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:08:07,827] [INFO] Task succeeded: Blastn
[2023-06-30 16:08:07,830] [INFO] Selected 13 target genomes.
[2023-06-30 16:08:07,830] [INFO] Target genome list was writen to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:08:07,843] [INFO] Task started: fastANI
[2023-06-30 16:08:07,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e76b2f2-695c-4b94-b5b6-977fb2d82817/GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna.gz --refList GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/target_genomes_gtdb.txt --output GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:08:12,029] [INFO] Task succeeded: fastANI
[2023-06-30 16:08:12,034] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:08:12,035] [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_009705435.1	s__Casp-actino8 sp009705435	96.2781	227	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.36	98.35	0.80	0.80	3	conclusive
GCA_014190215.1	s__Casp-actino8 sp014190215	93.4689	236	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694465.1	s__Casp-actino8 sp009694465	92.862	192	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	95.85	95.85	0.64	0.64	2	-
GCA_005801025.1	s__Casp-actino8 sp005801025	89.9926	193	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510335.1	s__Casp-actino8 sp001510335	78.6865	58	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872155.1	s__Casp-actino8 sp903872155	78.3498	97	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.87	96.83	0.92	0.86	4	-
GCA_009700145.1	s__Casp-actino8 sp009700145	77.522	71	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	99.51	99.42	0.81	0.73	6	-
--------------------------------------------------------------------------------
[2023-06-30 16:08:12,036] [INFO] GTDB search result was written to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/result_gtdb.tsv
[2023-06-30 16:08:12,037] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:08:12,039] [INFO] DFAST_QC result json was written to GCA_903906005.1_freshwater_MAG_---_Erken-D6_bin-0098_genomic.fna/dqc_result.json
[2023-06-30 16:08:12,039] [INFO] DFAST_QC completed!
[2023-06-30 16:08:12,039] [INFO] Total running time: 0h0m39s