[2023-03-18 21:50:26,955] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:50:26,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:50:26,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference
[2023-03-18 21:50:28,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:50:28,058] [INFO] Task started: Prodigal
[2023-03-18 21:50:28,058] [INFO] Running command: cat /var/lib/cwl/stg8e17d924-2825-499b-a377-ba9dd217285c/OceanDNA-b16509.fa | prodigal -d OceanDNA-b16509/cds.fna -a OceanDNA-b16509/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:50:36,912] [INFO] Task succeeded: Prodigal
[2023-03-18 21:50:36,912] [INFO] Task started: HMMsearch
[2023-03-18 21:50:36,912] [INFO] Running command: hmmsearch --tblout OceanDNA-b16509/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/reference_markers.hmm OceanDNA-b16509/protein.faa > /dev/null
[2023-03-18 21:50:37,046] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:50:37,046] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e17d924-2825-499b-a377-ba9dd217285c/OceanDNA-b16509.fa]
[2023-03-18 21:50:37,058] [INFO] Query marker FASTA was written to OceanDNA-b16509/markers.fasta
[2023-03-18 21:50:37,059] [INFO] Task started: Blastn
[2023-03-18 21:50:37,059] [INFO] Running command: blastn -query OceanDNA-b16509/markers.fasta -db /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/reference_markers.fasta -out OceanDNA-b16509/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:50:37,616] [INFO] Task succeeded: Blastn
[2023-03-18 21:50:37,617] [INFO] Selected 16 target genomes.
[2023-03-18 21:50:37,617] [INFO] Target genome list was writen to OceanDNA-b16509/target_genomes.txt
[2023-03-18 21:50:37,623] [INFO] Task started: fastANI
[2023-03-18 21:50:37,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e17d924-2825-499b-a377-ba9dd217285c/OceanDNA-b16509.fa --refList OceanDNA-b16509/target_genomes.txt --output OceanDNA-b16509/fastani_result.tsv --threads 1
[2023-03-18 21:50:46,662] [INFO] Task succeeded: fastANI
[2023-03-18 21:50:46,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:50:46,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:50:46,663] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:50:46,663] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:50:46,663] [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
--------------------------------------------------------------------------------
[2023-03-18 21:50:46,663] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16509/tc_result.tsv
[2023-03-18 21:50:46,663] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:50:46,663] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:50:46,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/checkm_data
[2023-03-18 21:50:46,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:50:46,669] [INFO] Task started: CheckM
[2023-03-18 21:50:46,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16509/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16509/checkm_input OceanDNA-b16509/checkm_result
[2023-03-18 21:51:15,832] [INFO] Task succeeded: CheckM
[2023-03-18 21:51:15,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.73%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:51:15,834] [INFO] ===== Completeness check finished =====
[2023-03-18 21:51:15,834] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:51:15,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16509/markers.fasta)
[2023-03-18 21:51:15,835] [INFO] Task started: Blastn
[2023-03-18 21:51:15,835] [INFO] Running command: blastn -query OceanDNA-b16509/markers.fasta -db /var/lib/cwl/stg65394e62-879e-4d9b-88cc-7586776ad830/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16509/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:51:16,583] [INFO] Task succeeded: Blastn
[2023-03-18 21:51:16,584] [INFO] Selected 7 target genomes.
[2023-03-18 21:51:16,584] [INFO] Target genome list was writen to OceanDNA-b16509/target_genomes_gtdb.txt
[2023-03-18 21:51:16,593] [INFO] Task started: fastANI
[2023-03-18 21:51:16,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e17d924-2825-499b-a377-ba9dd217285c/OceanDNA-b16509.fa --refList OceanDNA-b16509/target_genomes_gtdb.txt --output OceanDNA-b16509/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:51:19,046] [INFO] Task succeeded: fastANI
[2023-03-18 21:51:19,050] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:51:19,050] [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_003210315.1	s__Synechococcus_C sp003210315	97.6309	99	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.13	96.13	0.52	0.52	2	conclusive
GCF_000014585.1	s__Synechococcus_C sp000014585	89.5882	160	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040845.1	s__Synechococcus_C sp001040845	88.3735	161	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279775.1	s__Synechococcus_C sp002500205	87.8977	154	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	-
GCF_014279835.1	s__Synechococcus_C sp014279835	87.5711	156	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.93	96.36	0.92	0.87	4	-
GCF_000230675.1	s__Synechococcus_C sp000230675	86.8934	155	171	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.29	95.09	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2023-03-18 21:51:19,051] [INFO] GTDB search result was written to OceanDNA-b16509/result_gtdb.tsv
[2023-03-18 21:51:19,051] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:51:19,052] [INFO] DFAST_QC result json was written to OceanDNA-b16509/dqc_result.json
[2023-03-18 21:51:19,052] [INFO] DFAST_QC completed!
[2023-03-18 21:51:19,052] [INFO] Total running time: 0h0m52s