[2023-06-19 08:52:51,015] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:52:51,021] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:52:51,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference
[2023-06-19 08:52:52,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:52:52,370] [INFO] Task started: Prodigal
[2023-06-19 08:52:52,371] [INFO] Running command: gunzip -c /var/lib/cwl/stg80f41aa9-e27d-486a-a454-88606e55b312/GCA_018697995.1_ASM1869799v1_genomic.fna.gz | prodigal -d GCA_018697995.1_ASM1869799v1_genomic.fna/cds.fna -a GCA_018697995.1_ASM1869799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:52:55,988] [INFO] Task succeeded: Prodigal
[2023-06-19 08:52:55,988] [INFO] Task started: HMMsearch
[2023-06-19 08:52:55,989] [INFO] Running command: hmmsearch --tblout GCA_018697995.1_ASM1869799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/reference_markers.hmm GCA_018697995.1_ASM1869799v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:52:56,248] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:52:56,250] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg80f41aa9-e27d-486a-a454-88606e55b312/GCA_018697995.1_ASM1869799v1_genomic.fna.gz]
[2023-06-19 08:52:56,280] [INFO] Query marker FASTA was written to GCA_018697995.1_ASM1869799v1_genomic.fna/markers.fasta
[2023-06-19 08:52:56,280] [INFO] Task started: Blastn
[2023-06-19 08:52:56,280] [INFO] Running command: blastn -query GCA_018697995.1_ASM1869799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/reference_markers.fasta -out GCA_018697995.1_ASM1869799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:52:56,871] [INFO] Task succeeded: Blastn
[2023-06-19 08:52:56,876] [INFO] Selected 22 target genomes.
[2023-06-19 08:52:56,876] [INFO] Target genome list was writen to GCA_018697995.1_ASM1869799v1_genomic.fna/target_genomes.txt
[2023-06-19 08:52:56,912] [INFO] Task started: fastANI
[2023-06-19 08:52:56,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f41aa9-e27d-486a-a454-88606e55b312/GCA_018697995.1_ASM1869799v1_genomic.fna.gz --refList GCA_018697995.1_ASM1869799v1_genomic.fna/target_genomes.txt --output GCA_018697995.1_ASM1869799v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:53:09,638] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:09,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:53:09,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:53:09,646] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:53:09,646] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:53:09,646] [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
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	79.5826	360	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:53:09,648] [INFO] DFAST Taxonomy check result was written to GCA_018697995.1_ASM1869799v1_genomic.fna/tc_result.tsv
[2023-06-19 08:53:09,649] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:53:09,649] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:53:09,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/checkm_data
[2023-06-19 08:53:09,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:53:09,692] [INFO] Task started: CheckM
[2023-06-19 08:53:09,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018697995.1_ASM1869799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018697995.1_ASM1869799v1_genomic.fna/checkm_input GCA_018697995.1_ASM1869799v1_genomic.fna/checkm_result
[2023-06-19 08:53:28,923] [INFO] Task succeeded: CheckM
[2023-06-19 08:53:28,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:53:28,958] [INFO] ===== Completeness check finished =====
[2023-06-19 08:53:28,959] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:53:28,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018697995.1_ASM1869799v1_genomic.fna/markers.fasta)
[2023-06-19 08:53:28,960] [INFO] Task started: Blastn
[2023-06-19 08:53:28,960] [INFO] Running command: blastn -query GCA_018697995.1_ASM1869799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b9fcc6-acc2-4da3-8016-80c7dd9e6bff/dqc_reference/reference_markers_gtdb.fasta -out GCA_018697995.1_ASM1869799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:53:29,839] [INFO] Task succeeded: Blastn
[2023-06-19 08:53:29,845] [INFO] Selected 9 target genomes.
[2023-06-19 08:53:29,845] [INFO] Target genome list was writen to GCA_018697995.1_ASM1869799v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:53:29,877] [INFO] Task started: fastANI
[2023-06-19 08:53:29,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f41aa9-e27d-486a-a454-88606e55b312/GCA_018697995.1_ASM1869799v1_genomic.fna.gz --refList GCA_018697995.1_ASM1869799v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018697995.1_ASM1869799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:53:35,338] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:35,353] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:53:35,353] [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_012960135.1	s__Methyloprofundus sp012960135	97.9636	474	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	98.32	97.92	0.84	0.80	9	conclusive
GCF_002072955.1	s__Methyloprofundus sedimenti	79.5826	360	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002189065.1	s__Methyloprofundus sp002189065	79.3416	297	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016592635.1	s__Methyloprofundus sp016592635	78.0837	157	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138555.1	s__Methyloprofundus sp013138555	77.7667	162	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128525.1	s__Methyloprofundus sp900128525	77.4459	131	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859465.1	s__Methyloprofundus sp014859465	77.4039	149	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138595.1	s__Methyloprofundus sp013138595	76.9796	105	565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:53:35,356] [INFO] GTDB search result was written to GCA_018697995.1_ASM1869799v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:53:35,357] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:53:35,360] [INFO] DFAST_QC result json was written to GCA_018697995.1_ASM1869799v1_genomic.fna/dqc_result.json
[2023-06-19 08:53:35,360] [INFO] DFAST_QC completed!
[2023-06-19 08:53:35,360] [INFO] Total running time: 0h0m44s