[2023-03-19 01:33:27,260] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference
[2023-03-19 01:33:28,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,377] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,378] [INFO] Running command: cat /var/lib/cwl/stg1ca42115-fbea-4263-88ef-65bfd54cee66/OceanDNA-b45904.fa | prodigal -d OceanDNA-b45904/cds.fna -a OceanDNA-b45904/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:36,481] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:36,481] [INFO] Task started: HMMsearch
[2023-03-19 01:33:36,481] [INFO] Running command: hmmsearch --tblout OceanDNA-b45904/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/reference_markers.hmm OceanDNA-b45904/protein.faa > /dev/null
[2023-03-19 01:33:36,648] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:36,648] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ca42115-fbea-4263-88ef-65bfd54cee66/OceanDNA-b45904.fa]
[2023-03-19 01:33:36,659] [INFO] Query marker FASTA was written to OceanDNA-b45904/markers.fasta
[2023-03-19 01:33:36,661] [INFO] Task started: Blastn
[2023-03-19 01:33:36,661] [INFO] Running command: blastn -query OceanDNA-b45904/markers.fasta -db /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/reference_markers.fasta -out OceanDNA-b45904/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:37,230] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:37,231] [INFO] Selected 20 target genomes.
[2023-03-19 01:33:37,231] [INFO] Target genome list was writen to OceanDNA-b45904/target_genomes.txt
[2023-03-19 01:33:37,246] [INFO] Task started: fastANI
[2023-03-19 01:33:37,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca42115-fbea-4263-88ef-65bfd54cee66/OceanDNA-b45904.fa --refList OceanDNA-b45904/target_genomes.txt --output OceanDNA-b45904/fastani_result.tsv --threads 1
[2023-03-19 01:33:50,208] [INFO] Task succeeded: fastANI
[2023-03-19 01:33:50,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:33:50,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:33:50,208] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:33:50,208] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:33:50,209] [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
--------------------------------------------------------------------------------
[2023-03-19 01:33:50,209] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45904/tc_result.tsv
[2023-03-19 01:33:50,209] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:33:50,209] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:33:50,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/checkm_data
[2023-03-19 01:33:50,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:33:50,239] [INFO] Task started: CheckM
[2023-03-19 01:33:50,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45904/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45904/checkm_input OceanDNA-b45904/checkm_result
[2023-03-19 01:34:16,615] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:16,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:16,617] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:16,617] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:16,617] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45904/markers.fasta)
[2023-03-19 01:34:16,618] [INFO] Task started: Blastn
[2023-03-19 01:34:16,618] [INFO] Running command: blastn -query OceanDNA-b45904/markers.fasta -db /var/lib/cwl/stg87637f31-6180-4a81-b6ce-b0486c53f3ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45904/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:17,563] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:17,564] [INFO] Selected 8 target genomes.
[2023-03-19 01:34:17,564] [INFO] Target genome list was writen to OceanDNA-b45904/target_genomes_gtdb.txt
[2023-03-19 01:34:17,573] [INFO] Task started: fastANI
[2023-03-19 01:34:17,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca42115-fbea-4263-88ef-65bfd54cee66/OceanDNA-b45904.fa --refList OceanDNA-b45904/target_genomes_gtdb.txt --output OceanDNA-b45904/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:34:20,755] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:20,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:34:20,761] [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_905182465.1	s__UBA7441 sp905182465	98.265	249	270	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009886465.1	s__UBA7441 sp009886465	92.6746	232	270	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_003331195.1	s__UBA7441 sp003331195	90.7918	221	270	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	89.0523	241	270	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	87.3763	225	270	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_002729725.1	s__UBA7441 sp002729725	79.0451	80	270	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCA_002480015.1	s__UBA7441 sp002480015	77.56	95	270	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	-
GCA_018607135.1	s__BACL24 sp003485085	77.4853	53	270	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:34:20,761] [INFO] GTDB search result was written to OceanDNA-b45904/result_gtdb.tsv
[2023-03-19 01:34:20,761] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:34:20,762] [INFO] DFAST_QC result json was written to OceanDNA-b45904/dqc_result.json
[2023-03-19 01:34:20,762] [INFO] DFAST_QC completed!
[2023-03-19 01:34:20,762] [INFO] Total running time: 0h0m54s