[2023-03-15 14:29:06,036] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference
[2023-03-15 14:29:07,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,144] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,144] [INFO] Running command: cat /var/lib/cwl/stge72295ed-2e09-47fd-a786-51cdfcec4088/OceanDNA-b10936.fa | prodigal -d OceanDNA-b10936/cds.fna -a OceanDNA-b10936/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:15,845] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:15,845] [INFO] Task started: HMMsearch
[2023-03-15 14:29:15,846] [INFO] Running command: hmmsearch --tblout OceanDNA-b10936/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/reference_markers.hmm OceanDNA-b10936/protein.faa > /dev/null
[2023-03-15 14:29:16,009] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:16,009] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge72295ed-2e09-47fd-a786-51cdfcec4088/OceanDNA-b10936.fa]
[2023-03-15 14:29:16,021] [INFO] Query marker FASTA was written to OceanDNA-b10936/markers.fasta
[2023-03-15 14:29:16,022] [INFO] Task started: Blastn
[2023-03-15 14:29:16,022] [INFO] Running command: blastn -query OceanDNA-b10936/markers.fasta -db /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/reference_markers.fasta -out OceanDNA-b10936/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:16,571] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:16,571] [INFO] Selected 26 target genomes.
[2023-03-15 14:29:16,572] [INFO] Target genome list was writen to OceanDNA-b10936/target_genomes.txt
[2023-03-15 14:29:16,585] [INFO] Task started: fastANI
[2023-03-15 14:29:16,585] [INFO] Running command: fastANI --query /var/lib/cwl/stge72295ed-2e09-47fd-a786-51cdfcec4088/OceanDNA-b10936.fa --refList OceanDNA-b10936/target_genomes.txt --output OceanDNA-b10936/fastani_result.tsv --threads 1
[2023-03-15 14:29:32,170] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:32,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:32,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:32,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:32,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:29:32,171] [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
--------------------------------------------------------------------------------
[2023-03-15 14:29:32,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10936/tc_result.tsv
[2023-03-15 14:29:32,171] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:32,171] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:32,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/checkm_data
[2023-03-15 14:29:32,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:32,178] [INFO] Task started: CheckM
[2023-03-15 14:29:32,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10936/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10936/checkm_input OceanDNA-b10936/checkm_result
[2023-03-15 14:29:59,149] [INFO] Task succeeded: CheckM
[2023-03-15 14:29:59,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:29:59,190] [INFO] ===== Completeness check finished =====
[2023-03-15 14:29:59,190] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:29:59,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10936/markers.fasta)
[2023-03-15 14:29:59,192] [INFO] Task started: Blastn
[2023-03-15 14:29:59,192] [INFO] Running command: blastn -query OceanDNA-b10936/markers.fasta -db /var/lib/cwl/stgd9ce834f-215b-4e8c-9386-6b1dcfdaf9ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10936/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:59,955] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:59,956] [INFO] Selected 24 target genomes.
[2023-03-15 14:29:59,956] [INFO] Target genome list was writen to OceanDNA-b10936/target_genomes_gtdb.txt
[2023-03-15 14:30:00,002] [INFO] Task started: fastANI
[2023-03-15 14:30:00,002] [INFO] Running command: fastANI --query /var/lib/cwl/stge72295ed-2e09-47fd-a786-51cdfcec4088/OceanDNA-b10936.fa --refList OceanDNA-b10936/target_genomes_gtdb.txt --output OceanDNA-b10936/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:30:12,177] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:12,182] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:30:12,182] [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_905478905.1	s__UBA7428 sp905478905	77.699	112	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526275.1	s__UBA7428 sp011526275	77.6395	111	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526285.1	s__UBA7428 sp011526285	77.5484	135	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526335.1	s__UBA7428 sp011526335	77.0561	59	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526265.1	s__UBA7428 sp011526265	76.7909	66	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023645.1	s__UBA7428 sp003023645	76.6851	58	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_905181615.1	s__UBA7428 sp905181615	76.5708	51	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:30:12,182] [INFO] GTDB search result was written to OceanDNA-b10936/result_gtdb.tsv
[2023-03-15 14:30:12,182] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:30:12,183] [INFO] DFAST_QC result json was written to OceanDNA-b10936/dqc_result.json
[2023-03-15 14:30:12,183] [INFO] DFAST_QC completed!
[2023-03-15 14:30:12,183] [INFO] Total running time: 0h1m6s