[2023-03-16 18:09:00,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:09:00,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:09:00,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference
[2023-03-16 18:09:01,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:09:01,193] [INFO] Task started: Prodigal
[2023-03-16 18:09:01,193] [INFO] Running command: cat /var/lib/cwl/stg2edda1f8-4fea-4b1d-a034-f8f730dbf371/OceanDNA-b27491.fa | prodigal -d OceanDNA-b27491/cds.fna -a OceanDNA-b27491/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:09:07,568] [INFO] Task succeeded: Prodigal
[2023-03-16 18:09:07,568] [INFO] Task started: HMMsearch
[2023-03-16 18:09:07,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b27491/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/reference_markers.hmm OceanDNA-b27491/protein.faa > /dev/null
[2023-03-16 18:09:07,730] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:09:07,731] [INFO] Found 6/6 markers.
[2023-03-16 18:09:07,740] [INFO] Query marker FASTA was written to OceanDNA-b27491/markers.fasta
[2023-03-16 18:09:07,740] [INFO] Task started: Blastn
[2023-03-16 18:09:07,740] [INFO] Running command: blastn -query OceanDNA-b27491/markers.fasta -db /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/reference_markers.fasta -out OceanDNA-b27491/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:08,295] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:08,296] [INFO] Selected 25 target genomes.
[2023-03-16 18:09:08,296] [INFO] Target genome list was writen to OceanDNA-b27491/target_genomes.txt
[2023-03-16 18:09:08,305] [INFO] Task started: fastANI
[2023-03-16 18:09:08,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edda1f8-4fea-4b1d-a034-f8f730dbf371/OceanDNA-b27491.fa --refList OceanDNA-b27491/target_genomes.txt --output OceanDNA-b27491/fastani_result.tsv --threads 1
[2023-03-16 18:09:16,081] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:16,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:09:16,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:09:16,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:09:16,082] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:09:16,082] [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
--------------------------------------------------------------------------------
[2023-03-16 18:09:16,082] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27491/tc_result.tsv
[2023-03-16 18:09:16,082] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:09:16,082] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:09:16,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/checkm_data
[2023-03-16 18:09:16,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:09:16,087] [INFO] Task started: CheckM
[2023-03-16 18:09:16,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27491/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27491/checkm_input OceanDNA-b27491/checkm_result
[2023-03-16 18:09:37,115] [INFO] Task succeeded: CheckM
[2023-03-16 18:09:37,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:09:37,117] [INFO] ===== Completeness check finished =====
[2023-03-16 18:09:37,117] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:09:37,118] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27491/markers.fasta)
[2023-03-16 18:09:37,119] [INFO] Task started: Blastn
[2023-03-16 18:09:37,119] [INFO] Running command: blastn -query OceanDNA-b27491/markers.fasta -db /var/lib/cwl/stg2a1ca539-b0b3-419b-8b8d-5bc7189889be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27491/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:38,051] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:38,052] [INFO] Selected 25 target genomes.
[2023-03-16 18:09:38,052] [INFO] Target genome list was writen to OceanDNA-b27491/target_genomes_gtdb.txt
[2023-03-16 18:09:38,109] [INFO] Task started: fastANI
[2023-03-16 18:09:38,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edda1f8-4fea-4b1d-a034-f8f730dbf371/OceanDNA-b27491.fa --refList OceanDNA-b27491/target_genomes_gtdb.txt --output OceanDNA-b27491/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:43,591] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:43,595] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:09:43,595] [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_002704755.1	s__TMED25 sp002704755	99.2929	400	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_016780665.1	s__TMED25 sp016780665	94.5364	253	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.95	99.95	0.98	0.98	2	-
GCA_902613795.1	s__TMED25 sp902613795	77.0092	90	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.47	99.34	0.93	0.93	3	-
GCA_902632055.1	s__TMED25 sp902632055	76.8217	74	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002168075.1	s__TMED25 sp002168075	76.224	92	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.97	97.02	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:43,595] [INFO] GTDB search result was written to OceanDNA-b27491/result_gtdb.tsv
[2023-03-16 18:09:43,595] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:43,596] [INFO] DFAST_QC result json was written to OceanDNA-b27491/dqc_result.json
[2023-03-16 18:09:43,596] [INFO] DFAST_QC completed!
[2023-03-16 18:09:43,596] [INFO] Total running time: 0h0m44s