[2023-06-05 10:36:25,581] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:36:25,587] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:36:25,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference
[2023-06-05 10:36:28,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:36:28,617] [INFO] Task started: Prodigal
[2023-06-05 10:36:28,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg3567c912-6d77-4838-8e4c-4aa485bc1830/GCA_001774635.1_ASM177463v1_genomic.fna.gz | prodigal -d GCA_001774635.1_ASM177463v1_genomic.fna/cds.fna -a GCA_001774635.1_ASM177463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:36:34,000] [INFO] Task succeeded: Prodigal
[2023-06-05 10:36:34,000] [INFO] Task started: HMMsearch
[2023-06-05 10:36:34,000] [INFO] Running command: hmmsearch --tblout GCA_001774635.1_ASM177463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/reference_markers.hmm GCA_001774635.1_ASM177463v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:36:34,240] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:36:34,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3567c912-6d77-4838-8e4c-4aa485bc1830/GCA_001774635.1_ASM177463v1_genomic.fna.gz]
[2023-06-05 10:36:34,260] [INFO] Query marker FASTA was written to GCA_001774635.1_ASM177463v1_genomic.fna/markers.fasta
[2023-06-05 10:36:34,261] [INFO] Task started: Blastn
[2023-06-05 10:36:34,261] [INFO] Running command: blastn -query GCA_001774635.1_ASM177463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/reference_markers.fasta -out GCA_001774635.1_ASM177463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:36:34,850] [INFO] Task succeeded: Blastn
[2023-06-05 10:36:34,855] [INFO] Selected 11 target genomes.
[2023-06-05 10:36:34,855] [INFO] Target genome list was writen to GCA_001774635.1_ASM177463v1_genomic.fna/target_genomes.txt
[2023-06-05 10:36:34,860] [INFO] Task started: fastANI
[2023-06-05 10:36:34,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg3567c912-6d77-4838-8e4c-4aa485bc1830/GCA_001774635.1_ASM177463v1_genomic.fna.gz --refList GCA_001774635.1_ASM177463v1_genomic.fna/target_genomes.txt --output GCA_001774635.1_ASM177463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:36:40,825] [INFO] Task succeeded: fastANI
[2023-06-05 10:36:40,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:36:40,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:36:40,829] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:36:40,829] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:36:40,830] [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
--------------------------------------------------------------------------------
[2023-06-05 10:36:40,832] [INFO] DFAST Taxonomy check result was written to GCA_001774635.1_ASM177463v1_genomic.fna/tc_result.tsv
[2023-06-05 10:36:40,833] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:36:40,833] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:36:40,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/checkm_data
[2023-06-05 10:36:40,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:36:40,861] [INFO] Task started: CheckM
[2023-06-05 10:36:40,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001774635.1_ASM177463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001774635.1_ASM177463v1_genomic.fna/checkm_input GCA_001774635.1_ASM177463v1_genomic.fna/checkm_result
[2023-06-05 10:37:03,373] [INFO] Task succeeded: CheckM
[2023-06-05 10:37:03,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:37:03,394] [INFO] ===== Completeness check finished =====
[2023-06-05 10:37:03,394] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:37:03,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001774635.1_ASM177463v1_genomic.fna/markers.fasta)
[2023-06-05 10:37:03,395] [INFO] Task started: Blastn
[2023-06-05 10:37:03,395] [INFO] Running command: blastn -query GCA_001774635.1_ASM177463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78237a97-fae6-40da-a24d-427d3f53d91a/dqc_reference/reference_markers_gtdb.fasta -out GCA_001774635.1_ASM177463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:37:04,141] [INFO] Task succeeded: Blastn
[2023-06-05 10:37:04,145] [INFO] Selected 13 target genomes.
[2023-06-05 10:37:04,145] [INFO] Target genome list was writen to GCA_001774635.1_ASM177463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:37:04,154] [INFO] Task started: fastANI
[2023-06-05 10:37:04,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg3567c912-6d77-4838-8e4c-4aa485bc1830/GCA_001774635.1_ASM177463v1_genomic.fna.gz --refList GCA_001774635.1_ASM177463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001774635.1_ASM177463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:37:08,025] [INFO] Task succeeded: fastANI
[2023-06-05 10:37:08,033] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:37:08,033] [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_001774685.1	s__UBA10133 sp001774685	99.9996	363	363	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.99	99.98	0.99	0.97	7	conclusive
GCA_003531665.1	s__UBA10133 sp003531665	81.6112	170	363	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.84	99.79	0.92	0.85	7	-
GCA_002789895.1	s__UBA10133 sp002789895	81.1546	157	363	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.55	99.43	0.85	0.81	5	-
GCA_001000865.1	s__UBA10133 sp001000865	80.8019	172	363	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001001485.1	s__UBA10133 sp001001485	77.0257	67	363	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.94	99.92	0.97	0.92	6	-
--------------------------------------------------------------------------------
[2023-06-05 10:37:08,035] [INFO] GTDB search result was written to GCA_001774635.1_ASM177463v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:37:08,036] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:37:08,038] [INFO] DFAST_QC result json was written to GCA_001774635.1_ASM177463v1_genomic.fna/dqc_result.json
[2023-06-05 10:37:08,039] [INFO] DFAST_QC completed!
[2023-06-05 10:37:08,039] [INFO] Total running time: 0h0m42s