[2023-03-16 06:12:59,354] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:59,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:59,355] [INFO] DQC Reference Directory: /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference
[2023-03-16 06:13:00,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:13:00,437] [INFO] Task started: Prodigal
[2023-03-16 06:13:00,437] [INFO] Running command: cat /var/lib/cwl/stg84df91a4-46d2-4f54-a4d6-d7e959e795c1/OceanDNA-b12799.fa | prodigal -d OceanDNA-b12799/cds.fna -a OceanDNA-b12799/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:13:12,402] [INFO] Task succeeded: Prodigal
[2023-03-16 06:13:12,402] [INFO] Task started: HMMsearch
[2023-03-16 06:13:12,402] [INFO] Running command: hmmsearch --tblout OceanDNA-b12799/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/reference_markers.hmm OceanDNA-b12799/protein.faa > /dev/null
[2023-03-16 06:13:12,568] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:13:12,569] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg84df91a4-46d2-4f54-a4d6-d7e959e795c1/OceanDNA-b12799.fa]
[2023-03-16 06:13:12,584] [INFO] Query marker FASTA was written to OceanDNA-b12799/markers.fasta
[2023-03-16 06:13:12,584] [INFO] Task started: Blastn
[2023-03-16 06:13:12,584] [INFO] Running command: blastn -query OceanDNA-b12799/markers.fasta -db /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/reference_markers.fasta -out OceanDNA-b12799/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:13,085] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:13,086] [INFO] Selected 24 target genomes.
[2023-03-16 06:13:13,086] [INFO] Target genome list was writen to OceanDNA-b12799/target_genomes.txt
[2023-03-16 06:13:13,097] [INFO] Task started: fastANI
[2023-03-16 06:13:13,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg84df91a4-46d2-4f54-a4d6-d7e959e795c1/OceanDNA-b12799.fa --refList OceanDNA-b12799/target_genomes.txt --output OceanDNA-b12799/fastani_result.tsv --threads 1
[2023-03-16 06:13:26,410] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:26,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:13:26,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:13:26,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:13:26,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:13:26,411] [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 06:13:26,412] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12799/tc_result.tsv
[2023-03-16 06:13:26,412] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:13:26,412] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:13:26,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/checkm_data
[2023-03-16 06:13:26,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:13:26,549] [INFO] Task started: CheckM
[2023-03-16 06:13:26,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12799/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12799/checkm_input OceanDNA-b12799/checkm_result
[2023-03-16 06:14:00,038] [INFO] Task succeeded: CheckM
[2023-03-16 06:14:00,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:14:00,041] [INFO] ===== Completeness check finished =====
[2023-03-16 06:14:00,041] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:14:00,042] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12799/markers.fasta)
[2023-03-16 06:14:00,043] [INFO] Task started: Blastn
[2023-03-16 06:14:00,043] [INFO] Running command: blastn -query OceanDNA-b12799/markers.fasta -db /var/lib/cwl/stged56a92b-9a4b-4c1d-895f-53e0a35b750c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12799/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:14:00,711] [INFO] Task succeeded: Blastn
[2023-03-16 06:14:00,712] [INFO] Selected 16 target genomes.
[2023-03-16 06:14:00,712] [INFO] Target genome list was writen to OceanDNA-b12799/target_genomes_gtdb.txt
[2023-03-16 06:14:00,735] [INFO] Task started: fastANI
[2023-03-16 06:14:00,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg84df91a4-46d2-4f54-a4d6-d7e959e795c1/OceanDNA-b12799.fa --refList OceanDNA-b12799/target_genomes_gtdb.txt --output OceanDNA-b12799/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:14:07,473] [INFO] Task succeeded: fastANI
[2023-03-16 06:14:07,478] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:14:07,478] [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_003484585.1	s__UBA9320 sp003484585	79.9955	163	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	95.66	95.66	0.53	0.53	2	-
GCA_003485825.1	s__UBA9320 sp003485825	79.6953	225	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700895.1	s__UBA9320 sp018700895	77.1529	107	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857855.1	s__UBA9320 sp003516975	76.8262	69	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.31	99.21	0.89	0.84	3	-
GCA_002746305.1	s__UBA9320 sp002746305	76.6917	108	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402155.1	s__UBA9320 sp018402155	76.6423	87	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:14:07,478] [INFO] GTDB search result was written to OceanDNA-b12799/result_gtdb.tsv
[2023-03-16 06:14:07,478] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:14:07,480] [INFO] DFAST_QC result json was written to OceanDNA-b12799/dqc_result.json
[2023-03-16 06:14:07,481] [INFO] DFAST_QC completed!
[2023-03-16 06:14:07,481] [INFO] Total running time: 0h1m8s