[2023-03-15 10:52:57,306] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,318] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference
[2023-03-15 10:52:58,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,866] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,866] [INFO] Running command: cat /var/lib/cwl/stg74871e2d-fb88-4337-aed1-461eea169545/OceanDNA-a2560.fa | prodigal -d OceanDNA-a2560/cds.fna -a OceanDNA-a2560/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:09,969] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:09,970] [INFO] Task started: HMMsearch
[2023-03-15 10:53:09,970] [INFO] Running command: hmmsearch --tblout OceanDNA-a2560/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/reference_markers.hmm OceanDNA-a2560/protein.faa > /dev/null
[2023-03-15 10:53:10,135] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:10,136] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg74871e2d-fb88-4337-aed1-461eea169545/OceanDNA-a2560.fa]
[2023-03-15 10:53:10,147] [INFO] Query marker FASTA was written to OceanDNA-a2560/markers.fasta
[2023-03-15 10:53:10,149] [INFO] Task started: Blastn
[2023-03-15 10:53:10,149] [INFO] Running command: blastn -query OceanDNA-a2560/markers.fasta -db /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/reference_markers.fasta -out OceanDNA-a2560/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:10,581] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:10,582] [INFO] Selected 3 target genomes.
[2023-03-15 10:53:10,582] [INFO] Target genome list was writen to OceanDNA-a2560/target_genomes.txt
[2023-03-15 10:53:10,585] [INFO] Task started: fastANI
[2023-03-15 10:53:10,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg74871e2d-fb88-4337-aed1-461eea169545/OceanDNA-a2560.fa --refList OceanDNA-a2560/target_genomes.txt --output OceanDNA-a2560/fastani_result.tsv --threads 1
[2023-03-15 10:53:11,813] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:11,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:11,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:11,813] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:11,813] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:11,814] [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 10:53:11,814] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2560/tc_result.tsv
[2023-03-15 10:53:11,814] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:11,814] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:11,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/checkm_data
[2023-03-15 10:53:11,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:11,870] [INFO] Task started: CheckM
[2023-03-15 10:53:11,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2560/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2560/checkm_input OceanDNA-a2560/checkm_result
[2023-03-15 10:53:44,390] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:44,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:44,392] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:44,392] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:44,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2560/markers.fasta)
[2023-03-15 10:53:44,393] [INFO] Task started: Blastn
[2023-03-15 10:53:44,393] [INFO] Running command: blastn -query OceanDNA-a2560/markers.fasta -db /var/lib/cwl/stgc0ba3943-be72-4912-a9ea-59b646d843e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2560/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:44,824] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:44,825] [INFO] Selected 9 target genomes.
[2023-03-15 10:53:44,825] [INFO] Target genome list was writen to OceanDNA-a2560/target_genomes_gtdb.txt
[2023-03-15 10:53:44,834] [INFO] Task started: fastANI
[2023-03-15 10:53:44,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg74871e2d-fb88-4337-aed1-461eea169545/OceanDNA-a2560.fa --refList OceanDNA-a2560/target_genomes_gtdb.txt --output OceanDNA-a2560/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:48,308] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:48,314] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:53:48,314] [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_002499705.1	s__MGIIa-L1 sp002499705	99.6746	508	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902520595.1	s__MGIIa-L1 sp902520595	89.0623	354	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170315.2	s__MGIIa-L1 sp002170315	84.2316	453	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937025.1	s__MGIIa-L1 sp009937025	79.4131	267	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182715.1	s__MGIIa-L1 sp905182715	78.8405	233	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182725.1	s__MGIIa-L1 sp905182725	78.7385	246	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182635.1	s__MGIIa-L1 sp905182635	78.4681	191	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687075.1	s__MGIIa-L1 sp002687075	77.5843	189	593	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:48,314] [INFO] GTDB search result was written to OceanDNA-a2560/result_gtdb.tsv
[2023-03-15 10:53:48,314] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:48,315] [INFO] DFAST_QC result json was written to OceanDNA-a2560/dqc_result.json
[2023-03-15 10:53:48,315] [INFO] DFAST_QC completed!
[2023-03-15 10:53:48,315] [INFO] Total running time: 0h0m51s