[2023-03-15 18:39:12,203] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,203] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,657] [INFO] Running command: cat /var/lib/cwl/stg070cc08a-ba89-4d54-b7e3-4b48ee0ee233/OceanDNA-b45913.fa | prodigal -d OceanDNA-b45913/cds.fna -a OceanDNA-b45913/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:19,168] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:19,168] [INFO] Task started: HMMsearch
[2023-03-15 18:39:19,168] [INFO] Running command: hmmsearch --tblout OceanDNA-b45913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/reference_markers.hmm OceanDNA-b45913/protein.faa > /dev/null
[2023-03-15 18:39:19,301] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:19,302] [INFO] Found 6/6 markers.
[2023-03-15 18:39:19,311] [INFO] Query marker FASTA was written to OceanDNA-b45913/markers.fasta
[2023-03-15 18:39:19,311] [INFO] Task started: Blastn
[2023-03-15 18:39:19,311] [INFO] Running command: blastn -query OceanDNA-b45913/markers.fasta -db /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/reference_markers.fasta -out OceanDNA-b45913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:19,823] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:19,824] [INFO] Selected 19 target genomes.
[2023-03-15 18:39:19,825] [INFO] Target genome list was writen to OceanDNA-b45913/target_genomes.txt
[2023-03-15 18:39:19,837] [INFO] Task started: fastANI
[2023-03-15 18:39:19,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg070cc08a-ba89-4d54-b7e3-4b48ee0ee233/OceanDNA-b45913.fa --refList OceanDNA-b45913/target_genomes.txt --output OceanDNA-b45913/fastani_result.tsv --threads 1
[2023-03-15 18:39:31,582] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:31,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:31,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:31,582] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:31,582] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:31,583] [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
--------------------------------------------------------------------------------
[2023-03-15 18:39:31,583] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45913/tc_result.tsv
[2023-03-15 18:39:31,583] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:31,583] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:31,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/checkm_data
[2023-03-15 18:39:31,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:31,590] [INFO] Task started: CheckM
[2023-03-15 18:39:31,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45913/checkm_input OceanDNA-b45913/checkm_result
[2023-03-15 18:39:51,671] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:51,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:51,673] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:51,673] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:51,673] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45913/markers.fasta)
[2023-03-15 18:39:51,673] [INFO] Task started: Blastn
[2023-03-15 18:39:51,673] [INFO] Running command: blastn -query OceanDNA-b45913/markers.fasta -db /var/lib/cwl/stgc8d29692-54cf-41bc-96c1-0675e157b374/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:52,415] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:52,416] [INFO] Selected 7 target genomes.
[2023-03-15 18:39:52,416] [INFO] Target genome list was writen to OceanDNA-b45913/target_genomes_gtdb.txt
[2023-03-15 18:39:52,686] [INFO] Task started: fastANI
[2023-03-15 18:39:52,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg070cc08a-ba89-4d54-b7e3-4b48ee0ee233/OceanDNA-b45913.fa --refList OceanDNA-b45913/target_genomes_gtdb.txt --output OceanDNA-b45913/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:55,300] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:55,304] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:39:55,304] [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_009886465.1	s__UBA7441 sp009886465	94.5452	67	79	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	97.11	97.11	0.79	0.79	2	-
GCA_905182465.1	s__UBA7441 sp905182465	91.6455	64	79	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331195.1	s__UBA7441 sp003331195	90.9592	69	79	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862945.1	s__UBA7441 sp002862945	89.6756	72	79	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.18	98.18	0.82	0.82	2	-
GCA_902587165.1	s__UBA7441 sp902587165	87.2951	68	79	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:39:55,304] [INFO] GTDB search result was written to OceanDNA-b45913/result_gtdb.tsv
[2023-03-15 18:39:55,304] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:55,305] [INFO] DFAST_QC result json was written to OceanDNA-b45913/dqc_result.json
[2023-03-15 18:39:55,305] [INFO] DFAST_QC completed!
[2023-03-15 18:39:55,305] [INFO] Total running time: 0h0m43s