[2023-06-29 22:11:15,544] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:11:15,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:11:15,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference
[2023-06-29 22:11:16,787] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:11:16,788] [INFO] Task started: Prodigal
[2023-06-29 22:11:16,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg21d559d3-6c07-42c0-8c0b-5088067e6d5c/GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/cds.fna -a GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:11:24,616] [INFO] Task succeeded: Prodigal
[2023-06-29 22:11:24,616] [INFO] Task started: HMMsearch
[2023-06-29 22:11:24,616] [INFO] Running command: hmmsearch --tblout GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/reference_markers.hmm GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:11:24,843] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:11:24,845] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg21d559d3-6c07-42c0-8c0b-5088067e6d5c/GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna.gz]
[2023-06-29 22:11:24,867] [INFO] Query marker FASTA was written to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-29 22:11:24,868] [INFO] Task started: Blastn
[2023-06-29 22:11:24,868] [INFO] Running command: blastn -query GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/reference_markers.fasta -out GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:11:25,427] [INFO] Task succeeded: Blastn
[2023-06-29 22:11:25,432] [INFO] Selected 9 target genomes.
[2023-06-29 22:11:25,432] [INFO] Target genome list was writen to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-29 22:11:25,434] [INFO] Task started: fastANI
[2023-06-29 22:11:25,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d559d3-6c07-42c0-8c0b-5088067e6d5c/GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna.gz --refList GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:11:32,000] [INFO] Task succeeded: fastANI
[2023-06-29 22:11:32,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:11:32,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:11:32,003] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:11:32,003] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:11:32,004] [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 22:11:32,006] [INFO] DFAST Taxonomy check result was written to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-29 22:11:32,007] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:11:32,007] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:11:32,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/checkm_data
[2023-06-29 22:11:32,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:11:32,030] [INFO] Task started: CheckM
[2023-06-29 22:11:32,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/checkm_input GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/checkm_result
[2023-06-29 22:12:00,837] [INFO] Task succeeded: CheckM
[2023-06-29 22:12:00,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:12:00,859] [INFO] ===== Completeness check finished =====
[2023-06-29 22:12:00,859] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:12:00,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-29 22:12:00,860] [INFO] Task started: Blastn
[2023-06-29 22:12:00,860] [INFO] Running command: blastn -query GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f4c940-d683-4b06-94d4-eb7db4f4a0e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:12:01,695] [INFO] Task succeeded: Blastn
[2023-06-29 22:12:01,700] [INFO] Selected 11 target genomes.
[2023-06-29 22:12:01,700] [INFO] Target genome list was writen to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:12:01,703] [INFO] Task started: fastANI
[2023-06-29 22:12:01,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d559d3-6c07-42c0-8c0b-5088067e6d5c/GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna.gz --refList GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:12:07,469] [INFO] Task succeeded: fastANI
[2023-06-29 22:12:07,476] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-29 22:12:07,477] [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_017857425.1	s__UBA985 sp017857425	97.5454	354	456	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	96.59	96.59	0.83	0.83	2	inconclusive
GCA_002292185.1	s__UBA985 sp002292185	95.3843	335	456	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.24	97.16	0.73	0.70	3	inconclusive
GCA_009937455.1	s__UBA985 sp009937455	90.7665	306	456	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	77.3745	69	456	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_013041925.1	s__UBA985 sp013041925	77.0767	78	456	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 22:12:07,479] [INFO] GTDB search result was written to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-29 22:12:07,479] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:12:07,482] [INFO] DFAST_QC result json was written to GCA_943844845.1_20200430_METABAT_129_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-29 22:12:07,482] [INFO] DFAST_QC completed!
[2023-06-29 22:12:07,482] [INFO] Total running time: 0h0m52s