[2023-03-17 09:05:02,568] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,569] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference
[2023-03-17 09:05:03,729] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,730] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,730] [INFO] Running command: cat /var/lib/cwl/stg9ff8131a-3ed2-43fb-8315-b93452d8f53c/OceanDNA-b347.fa | prodigal -d OceanDNA-b347/cds.fna -a OceanDNA-b347/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:12,021] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:12,022] [INFO] Task started: HMMsearch
[2023-03-17 09:05:12,022] [INFO] Running command: hmmsearch --tblout OceanDNA-b347/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/reference_markers.hmm OceanDNA-b347/protein.faa > /dev/null
[2023-03-17 09:05:12,187] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:12,188] [INFO] Found 6/6 markers.
[2023-03-17 09:05:12,201] [INFO] Query marker FASTA was written to OceanDNA-b347/markers.fasta
[2023-03-17 09:05:12,202] [INFO] Task started: Blastn
[2023-03-17 09:05:12,202] [INFO] Running command: blastn -query OceanDNA-b347/markers.fasta -db /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/reference_markers.fasta -out OceanDNA-b347/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:12,733] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:12,734] [INFO] Selected 20 target genomes.
[2023-03-17 09:05:12,734] [INFO] Target genome list was writen to OceanDNA-b347/target_genomes.txt
[2023-03-17 09:05:12,873] [INFO] Task started: fastANI
[2023-03-17 09:05:12,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff8131a-3ed2-43fb-8315-b93452d8f53c/OceanDNA-b347.fa --refList OceanDNA-b347/target_genomes.txt --output OceanDNA-b347/fastani_result.tsv --threads 1
[2023-03-17 09:05:25,547] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:25,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:25,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:25,548] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:25,548] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:25,548] [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
--------------------------------------------------------------------------------
[2023-03-17 09:05:25,548] [INFO] DFAST Taxonomy check result was written to OceanDNA-b347/tc_result.tsv
[2023-03-17 09:05:25,548] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:25,548] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:25,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/checkm_data
[2023-03-17 09:05:25,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:25,562] [INFO] Task started: CheckM
[2023-03-17 09:05:25,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b347/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b347/checkm_input OceanDNA-b347/checkm_result
[2023-03-17 09:05:51,611] [INFO] Task succeeded: CheckM
[2023-03-17 09:05:51,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:05:51,613] [INFO] ===== Completeness check finished =====
[2023-03-17 09:05:51,613] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:05:51,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b347/markers.fasta)
[2023-03-17 09:05:51,615] [INFO] Task started: Blastn
[2023-03-17 09:05:51,615] [INFO] Running command: blastn -query OceanDNA-b347/markers.fasta -db /var/lib/cwl/stg2d08bc51-d0e7-4418-a846-e129116a2730/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b347/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:52,357] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:52,358] [INFO] Selected 12 target genomes.
[2023-03-17 09:05:52,358] [INFO] Target genome list was writen to OceanDNA-b347/target_genomes_gtdb.txt
[2023-03-17 09:05:52,365] [INFO] Task started: fastANI
[2023-03-17 09:05:52,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff8131a-3ed2-43fb-8315-b93452d8f53c/OceanDNA-b347.fa --refList OceanDNA-b347/target_genomes_gtdb.txt --output OceanDNA-b347/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:05:55,489] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:55,496] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:05:55,496] [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_014190055.1	s__BACL27 sp014190055	89.1661	267	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	95.53	95.36	0.86	0.77	8	-
GCA_009927565.1	s__BACL27 sp009927565	85.4318	222	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737635.1	s__BACL27 sp002737635	82.4952	207	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003535455.1	s__BACL27 sp003535455	81.3121	230	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.51	98.35	0.83	0.76	7	-
GCA_009923685.1	s__BACL27 sp009923685	80.783	94	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005805045.1	s__BACL27 sp005805045	80.6614	187	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	99.25	99.23	0.81	0.81	3	-
GCA_016462185.1	s__BACL27 sp016462185	79.5869	214	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.92	98.92	0.88	0.88	2	-
GCA_014190295.1	s__BACL27 sp014190295	78.8339	169	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870935.1	s__BACL27 sp016870935	78.452	157	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463105.1	s__BACL27 sp016463105	78.0809	135	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871295.1	s__BACL27 sp016871295	77.7959	133	426	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:05:55,496] [INFO] GTDB search result was written to OceanDNA-b347/result_gtdb.tsv
[2023-03-17 09:05:55,496] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:05:55,497] [INFO] DFAST_QC result json was written to OceanDNA-b347/dqc_result.json
[2023-03-17 09:05:55,497] [INFO] DFAST_QC completed!
[2023-03-17 09:05:55,497] [INFO] Total running time: 0h0m53s