[2023-03-19 03:22:59,930] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,935] [INFO] DQC Reference Directory: /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference
[2023-03-19 03:23:01,021] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:01,021] [INFO] Task started: Prodigal
[2023-03-19 03:23:01,021] [INFO] Running command: cat /var/lib/cwl/stge9e5063d-bd39-4b3f-a2ce-684d5ff4bc3e/OceanDNA-b34093.fa | prodigal -d OceanDNA-b34093/cds.fna -a OceanDNA-b34093/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:03,748] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:03,748] [INFO] Task started: HMMsearch
[2023-03-19 03:23:03,748] [INFO] Running command: hmmsearch --tblout OceanDNA-b34093/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/reference_markers.hmm OceanDNA-b34093/protein.faa > /dev/null
[2023-03-19 03:23:03,898] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:03,899] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge9e5063d-bd39-4b3f-a2ce-684d5ff4bc3e/OceanDNA-b34093.fa]
[2023-03-19 03:23:03,961] [INFO] Query marker FASTA was written to OceanDNA-b34093/markers.fasta
[2023-03-19 03:23:03,963] [INFO] Task started: Blastn
[2023-03-19 03:23:03,963] [INFO] Running command: blastn -query OceanDNA-b34093/markers.fasta -db /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/reference_markers.fasta -out OceanDNA-b34093/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:04,527] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:04,537] [INFO] Selected 22 target genomes.
[2023-03-19 03:23:04,537] [INFO] Target genome list was writen to OceanDNA-b34093/target_genomes.txt
[2023-03-19 03:23:04,549] [INFO] Task started: fastANI
[2023-03-19 03:23:04,549] [INFO] Running command: fastANI --query /var/lib/cwl/stge9e5063d-bd39-4b3f-a2ce-684d5ff4bc3e/OceanDNA-b34093.fa --refList OceanDNA-b34093/target_genomes.txt --output OceanDNA-b34093/fastani_result.tsv --threads 1
[2023-03-19 03:23:16,288] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:16,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:16,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:16,289] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:16,289] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:23:16,289] [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 03:23:16,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34093/tc_result.tsv
[2023-03-19 03:23:16,294] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:16,294] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:16,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/checkm_data
[2023-03-19 03:23:16,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:16,304] [INFO] Task started: CheckM
[2023-03-19 03:23:16,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34093/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34093/checkm_input OceanDNA-b34093/checkm_result
[2023-03-19 03:23:30,001] [INFO] Task succeeded: CheckM
[2023-03-19 03:23:30,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:23:30,249] [INFO] ===== Completeness check finished =====
[2023-03-19 03:23:30,249] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:23:30,249] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34093/markers.fasta)
[2023-03-19 03:23:30,249] [INFO] Task started: Blastn
[2023-03-19 03:23:30,249] [INFO] Running command: blastn -query OceanDNA-b34093/markers.fasta -db /var/lib/cwl/stga5f169f8-b859-4253-884a-8190bfa20179/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34093/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:30,910] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:30,920] [INFO] Selected 18 target genomes.
[2023-03-19 03:23:30,921] [INFO] Target genome list was writen to OceanDNA-b34093/target_genomes_gtdb.txt
[2023-03-19 03:23:30,970] [INFO] Task started: fastANI
[2023-03-19 03:23:30,970] [INFO] Running command: fastANI --query /var/lib/cwl/stge9e5063d-bd39-4b3f-a2ce-684d5ff4bc3e/OceanDNA-b34093.fa --refList OceanDNA-b34093/target_genomes_gtdb.txt --output OceanDNA-b34093/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:23:37,901] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:37,905] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:23:37,905] [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_014237605.1	s__GCA-2721545 sp014237605	95.2514	136	143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	95.61	95.61	0.87	0.87	2	conclusive
GCA_905612245.1	s__GCA-2721545 sp905612245	91.0146	84	143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721545.1	s__GCA-2721545 sp002721545	80.0967	121	143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	99.74	99.74	0.93	0.93	2	-
GCA_004525885.1	s__GCA-2721545 sp004525885	77.9195	84	143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003230615.1	s__GCA-2721545 sp003230615	76.5923	51	143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__GCA-2721545	95.0	97.47	97.47	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:23:37,906] [INFO] GTDB search result was written to OceanDNA-b34093/result_gtdb.tsv
[2023-03-19 03:23:37,909] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:23:37,910] [INFO] DFAST_QC result json was written to OceanDNA-b34093/dqc_result.json
[2023-03-19 03:23:37,910] [INFO] DFAST_QC completed!
[2023-03-19 03:23:37,910] [INFO] Total running time: 0h0m38s