[2023-03-18 08:55:50,665] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,665] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference
[2023-03-18 08:55:51,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,832] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,832] [INFO] Running command: cat /var/lib/cwl/stg5661d29b-cf78-43fc-b426-5b91c3eedb6a/OceanDNA-b15495.fa | prodigal -d OceanDNA-b15495/cds.fna -a OceanDNA-b15495/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:02,672] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:02,673] [INFO] Task started: HMMsearch
[2023-03-18 08:56:02,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b15495/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/reference_markers.hmm OceanDNA-b15495/protein.faa > /dev/null
[2023-03-18 08:56:02,899] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:02,899] [INFO] Found 6/6 markers.
[2023-03-18 08:56:02,916] [INFO] Query marker FASTA was written to OceanDNA-b15495/markers.fasta
[2023-03-18 08:56:02,923] [INFO] Task started: Blastn
[2023-03-18 08:56:02,923] [INFO] Running command: blastn -query OceanDNA-b15495/markers.fasta -db /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/reference_markers.fasta -out OceanDNA-b15495/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:03,499] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:03,500] [INFO] Selected 15 target genomes.
[2023-03-18 08:56:03,500] [INFO] Target genome list was writen to OceanDNA-b15495/target_genomes.txt
[2023-03-18 08:56:03,512] [INFO] Task started: fastANI
[2023-03-18 08:56:03,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg5661d29b-cf78-43fc-b426-5b91c3eedb6a/OceanDNA-b15495.fa --refList OceanDNA-b15495/target_genomes.txt --output OceanDNA-b15495/fastani_result.tsv --threads 1
[2023-03-18 08:56:13,860] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:13,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:13,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:13,861] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:13,861] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:13,861] [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 08:56:13,862] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15495/tc_result.tsv
[2023-03-18 08:56:13,862] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:13,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:13,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/checkm_data
[2023-03-18 08:56:13,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:13,901] [INFO] Task started: CheckM
[2023-03-18 08:56:13,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15495/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15495/checkm_input OceanDNA-b15495/checkm_result
[2023-03-18 08:56:45,140] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:45,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.24%
Contamintation: 7.64%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:45,144] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:45,144] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:45,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15495/markers.fasta)
[2023-03-18 08:56:45,145] [INFO] Task started: Blastn
[2023-03-18 08:56:45,145] [INFO] Running command: blastn -query OceanDNA-b15495/markers.fasta -db /var/lib/cwl/stg47016921-e69d-4ea3-b4b5-238d7c938d9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15495/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:45,902] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:45,904] [INFO] Selected 19 target genomes.
[2023-03-18 08:56:45,904] [INFO] Target genome list was writen to OceanDNA-b15495/target_genomes_gtdb.txt
[2023-03-18 08:56:45,942] [INFO] Task started: fastANI
[2023-03-18 08:56:45,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg5661d29b-cf78-43fc-b426-5b91c3eedb6a/OceanDNA-b15495.fa --refList OceanDNA-b15495/target_genomes_gtdb.txt --output OceanDNA-b15495/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:54,444] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:54,448] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:56:54,448] [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_009692925.1	s__SHYG01 sp009692925	76.533	83	599	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002238825.1	s__Bin87 sp002238825	76.1343	57	599	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872385.1	s__SHYG01 sp016872385	75.9401	90	599	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721995.1	s__UBA9611 sp002721995	75.6224	55	599	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:54,449] [INFO] GTDB search result was written to OceanDNA-b15495/result_gtdb.tsv
[2023-03-18 08:56:54,449] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:54,450] [INFO] DFAST_QC result json was written to OceanDNA-b15495/dqc_result.json
[2023-03-18 08:56:54,450] [INFO] DFAST_QC completed!
[2023-03-18 08:56:54,450] [INFO] Total running time: 0h1m4s