[2023-06-27 11:28:13,332] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:28:13,336] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:28:13,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference
[2023-06-27 11:28:14,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:28:14,639] [INFO] Task started: Prodigal
[2023-06-27 11:28:14,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg74088bea-1db9-49c4-90bf-dd64fdc5e2f9/GCA_026982355.1_ASM2698235v1_genomic.fna.gz | prodigal -d GCA_026982355.1_ASM2698235v1_genomic.fna/cds.fna -a GCA_026982355.1_ASM2698235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:28:21,050] [INFO] Task succeeded: Prodigal
[2023-06-27 11:28:21,050] [INFO] Task started: HMMsearch
[2023-06-27 11:28:21,051] [INFO] Running command: hmmsearch --tblout GCA_026982355.1_ASM2698235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/reference_markers.hmm GCA_026982355.1_ASM2698235v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:28:21,302] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:28:21,303] [INFO] Found 6/6 markers.
[2023-06-27 11:28:21,331] [INFO] Query marker FASTA was written to GCA_026982355.1_ASM2698235v1_genomic.fna/markers.fasta
[2023-06-27 11:28:21,332] [INFO] Task started: Blastn
[2023-06-27 11:28:21,332] [INFO] Running command: blastn -query GCA_026982355.1_ASM2698235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/reference_markers.fasta -out GCA_026982355.1_ASM2698235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:28:21,957] [INFO] Task succeeded: Blastn
[2023-06-27 11:28:21,961] [INFO] Selected 19 target genomes.
[2023-06-27 11:28:21,962] [INFO] Target genome list was writen to GCA_026982355.1_ASM2698235v1_genomic.fna/target_genomes.txt
[2023-06-27 11:28:21,966] [INFO] Task started: fastANI
[2023-06-27 11:28:21,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg74088bea-1db9-49c4-90bf-dd64fdc5e2f9/GCA_026982355.1_ASM2698235v1_genomic.fna.gz --refList GCA_026982355.1_ASM2698235v1_genomic.fna/target_genomes.txt --output GCA_026982355.1_ASM2698235v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:28:35,310] [INFO] Task succeeded: fastANI
[2023-06-27 11:28:35,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:28:35,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:28:35,313] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:28:35,313] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:28:35,313] [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
--------------------------------------------------------------------------------
[2023-06-27 11:28:35,316] [INFO] DFAST Taxonomy check result was written to GCA_026982355.1_ASM2698235v1_genomic.fna/tc_result.tsv
[2023-06-27 11:28:35,316] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:28:35,317] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:28:35,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/checkm_data
[2023-06-27 11:28:35,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:28:35,372] [INFO] Task started: CheckM
[2023-06-27 11:28:35,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026982355.1_ASM2698235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026982355.1_ASM2698235v1_genomic.fna/checkm_input GCA_026982355.1_ASM2698235v1_genomic.fna/checkm_result
[2023-06-27 11:29:01,367] [INFO] Task succeeded: CheckM
[2023-06-27 11:29:01,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:29:01,398] [INFO] ===== Completeness check finished =====
[2023-06-27 11:29:01,398] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:29:01,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026982355.1_ASM2698235v1_genomic.fna/markers.fasta)
[2023-06-27 11:29:01,400] [INFO] Task started: Blastn
[2023-06-27 11:29:01,400] [INFO] Running command: blastn -query GCA_026982355.1_ASM2698235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3833abc6-3c01-46da-8e30-1cabe34d9606/dqc_reference/reference_markers_gtdb.fasta -out GCA_026982355.1_ASM2698235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:29:02,386] [INFO] Task succeeded: Blastn
[2023-06-27 11:29:02,393] [INFO] Selected 17 target genomes.
[2023-06-27 11:29:02,394] [INFO] Target genome list was writen to GCA_026982355.1_ASM2698235v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:29:02,425] [INFO] Task started: fastANI
[2023-06-27 11:29:02,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg74088bea-1db9-49c4-90bf-dd64fdc5e2f9/GCA_026982355.1_ASM2698235v1_genomic.fna.gz --refList GCA_026982355.1_ASM2698235v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026982355.1_ASM2698235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:29:10,606] [INFO] Task succeeded: fastANI
[2023-06-27 11:29:10,614] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:29:10,614] [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_013152795.1	s__JAADFS01 sp013152795	88.9273	574	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__JAADFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491705.1	s__JAADFS01 sp015491705	86.3239	459	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__JAADFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897895.1	s__BMS3ABIN06 sp002897895	77.062	105	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__BMS3ABIN06	95.0	99.86	99.83	0.94	0.93	3	-
GCA_002897915.1	s__BMS3Abin09 sp002897915	76.2056	55	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__BMS3Abin09	95.0	99.52	99.52	0.93	0.93	2	-
GCA_003599505.1	s__SURF-23 sp003599505	76.171	51	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217725.1	s__SURF-23 sp016217725	75.8753	63	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599275.1	s__SURF-23 sp003599275	75.8682	52	818	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:29:10,616] [INFO] GTDB search result was written to GCA_026982355.1_ASM2698235v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:29:10,617] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:29:10,631] [INFO] DFAST_QC result json was written to GCA_026982355.1_ASM2698235v1_genomic.fna/dqc_result.json
[2023-06-27 11:29:10,632] [INFO] DFAST_QC completed!
[2023-06-27 11:29:10,632] [INFO] Total running time: 0h0m57s