[2023-06-17 14:32:39,385] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:32:39,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:32:39,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference
[2023-06-17 14:32:41,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:32:41,167] [INFO] Task started: Prodigal
[2023-06-17 14:32:41,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg07a4933b-6dbd-4856-935e-cd7ef36c3503/GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna.gz | prodigal -d GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/cds.fna -a GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:32:46,533] [INFO] Task succeeded: Prodigal
[2023-06-17 14:32:46,533] [INFO] Task started: HMMsearch
[2023-06-17 14:32:46,533] [INFO] Running command: hmmsearch --tblout GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/reference_markers.hmm GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:32:46,853] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:32:46,854] [INFO] Found 6/6 markers.
[2023-06-17 14:32:46,881] [INFO] Query marker FASTA was written to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/markers.fasta
[2023-06-17 14:32:46,882] [INFO] Task started: Blastn
[2023-06-17 14:32:46,882] [INFO] Running command: blastn -query GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/markers.fasta -db /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/reference_markers.fasta -out GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:32:47,531] [INFO] Task succeeded: Blastn
[2023-06-17 14:32:47,534] [INFO] Selected 23 target genomes.
[2023-06-17 14:32:47,535] [INFO] Target genome list was writen to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/target_genomes.txt
[2023-06-17 14:32:47,544] [INFO] Task started: fastANI
[2023-06-17 14:32:47,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a4933b-6dbd-4856-935e-cd7ef36c3503/GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna.gz --refList GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/target_genomes.txt --output GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:33:01,098] [INFO] Task succeeded: fastANI
[2023-06-17 14:33:01,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:33:01,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:33:01,100] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:33:01,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:33:01,101] [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
--------------------------------------------------------------------------------
[2023-06-17 14:33:01,103] [INFO] DFAST Taxonomy check result was written to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/tc_result.tsv
[2023-06-17 14:33:01,103] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:33:01,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:33:01,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/checkm_data
[2023-06-17 14:33:01,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:33:01,131] [INFO] Task started: CheckM
[2023-06-17 14:33:01,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/checkm_input GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/checkm_result
[2023-06-17 14:33:24,483] [INFO] Task succeeded: CheckM
[2023-06-17 14:33:24,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:33:24,504] [INFO] ===== Completeness check finished =====
[2023-06-17 14:33:24,504] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:33:24,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/markers.fasta)
[2023-06-17 14:33:24,505] [INFO] Task started: Blastn
[2023-06-17 14:33:24,505] [INFO] Running command: blastn -query GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/markers.fasta -db /var/lib/cwl/stg02bb7fc5-98d6-46b5-ac26-8860eb4adde0/dqc_reference/reference_markers_gtdb.fasta -out GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:33:25,334] [INFO] Task succeeded: Blastn
[2023-06-17 14:33:25,346] [INFO] Selected 14 target genomes.
[2023-06-17 14:33:25,346] [INFO] Target genome list was writen to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:33:25,354] [INFO] Task started: fastANI
[2023-06-17 14:33:25,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a4933b-6dbd-4856-935e-cd7ef36c3503/GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna.gz --refList GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/target_genomes_gtdb.txt --output GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:33:30,691] [INFO] Task succeeded: fastANI
[2023-06-17 14:33:30,704] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:33:30,704] [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_900548005.1	s__CAG-475 sp900548005	100.0	512	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	98.27	96.53	0.94	0.89	3	conclusive
GCA_900550915.1	s__CAG-475 sp900550915	88.5846	369	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	97.68	97.53	0.92	0.90	3	-
GCA_900769205.1	s__CAG-475 sp900769205	82.0226	218	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763875.1	s__CAG-475 sp900763875	80.7356	287	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549225.1	s__CAG-475 sp900549225	80.3929	250	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	99.88	99.88	0.96	0.96	2	-
GCA_000434435.1	s__CAG-475 sp000434435	80.2176	261	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	97.86	97.61	0.93	0.92	5	-
GCA_002449145.1	s__CAG-475 sp002449145	80.1942	249	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	98.71	98.37	0.92	0.89	8	-
GCA_002476605.1	s__CAG-475 sp002476605	80.1631	259	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550855.1	s__CAG-475 sp900550855	79.9951	232	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	100.00	100.00	0.97	0.97	2	-
GCA_900547975.1	s__CAG-475 sp900547975	79.9393	257	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	98.01	97.92	0.89	0.88	3	-
GCA_002478945.1	s__CAG-475 sp002478945	79.4044	238	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:33:30,707] [INFO] GTDB search result was written to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/result_gtdb.tsv
[2023-06-17 14:33:30,707] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:33:30,710] [INFO] DFAST_QC result json was written to GCA_905199045.1_ERR414265-mag-bin.10_genomic.fna/dqc_result.json
[2023-06-17 14:33:30,710] [INFO] DFAST_QC completed!
[2023-06-17 14:33:30,710] [INFO] Total running time: 0h0m51s