[2023-03-15 22:44:22,032] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,034] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,034] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference
[2023-03-15 22:44:23,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,187] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,187] [INFO] Running command: cat /var/lib/cwl/stg1f750322-ad4b-422a-8534-afffd8bd3ecb/OceanDNA-a1881.fa | prodigal -d OceanDNA-a1881/cds.fna -a OceanDNA-a1881/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:31,992] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:31,993] [INFO] Task started: HMMsearch
[2023-03-15 22:44:31,993] [INFO] Running command: hmmsearch --tblout OceanDNA-a1881/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/reference_markers.hmm OceanDNA-a1881/protein.faa > /dev/null
[2023-03-15 22:44:32,172] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:32,173] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1f750322-ad4b-422a-8534-afffd8bd3ecb/OceanDNA-a1881.fa]
[2023-03-15 22:44:32,199] [INFO] Query marker FASTA was written to OceanDNA-a1881/markers.fasta
[2023-03-15 22:44:32,200] [INFO] Task started: Blastn
[2023-03-15 22:44:32,200] [INFO] Running command: blastn -query OceanDNA-a1881/markers.fasta -db /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/reference_markers.fasta -out OceanDNA-a1881/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:32,652] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:32,656] [INFO] Selected 5 target genomes.
[2023-03-15 22:44:32,656] [INFO] Target genome list was writen to OceanDNA-a1881/target_genomes.txt
[2023-03-15 22:44:32,658] [INFO] Task started: fastANI
[2023-03-15 22:44:32,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f750322-ad4b-422a-8534-afffd8bd3ecb/OceanDNA-a1881.fa --refList OceanDNA-a1881/target_genomes.txt --output OceanDNA-a1881/fastani_result.tsv --threads 1
[2023-03-15 22:44:35,220] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:35,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:35,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:35,221] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:35,221] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:35,221] [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 22:44:35,224] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1881/tc_result.tsv
[2023-03-15 22:44:35,229] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:35,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:35,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/checkm_data
[2023-03-15 22:44:35,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:35,264] [INFO] Task started: CheckM
[2023-03-15 22:44:35,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1881/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1881/checkm_input OceanDNA-a1881/checkm_result
[2023-03-15 22:45:03,082] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:03,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:03,223] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:03,224] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:03,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1881/markers.fasta)
[2023-03-15 22:45:03,225] [INFO] Task started: Blastn
[2023-03-15 22:45:03,225] [INFO] Running command: blastn -query OceanDNA-a1881/markers.fasta -db /var/lib/cwl/stgc7d6817f-4002-4c5a-93d6-02f2fdc60e6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1881/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:03,774] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:03,790] [INFO] Selected 7 target genomes.
[2023-03-15 22:45:03,790] [INFO] Target genome list was writen to OceanDNA-a1881/target_genomes_gtdb.txt
[2023-03-15 22:45:03,851] [INFO] Task started: fastANI
[2023-03-15 22:45:03,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f750322-ad4b-422a-8534-afffd8bd3ecb/OceanDNA-a1881.fa --refList OceanDNA-a1881/target_genomes_gtdb.txt --output OceanDNA-a1881/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:06,143] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:06,148] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:06,149] [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_002689565.1	s__MGIIa-K1 sp002689565	93.2385	277	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715725.1	s__MGIIa-K1 sp002715725	79.3188	198	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	78.6322	207	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002710205.1	s__MGIIa-K1 sp002710205	78.5586	207	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	78.4892	203	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	78.3577	191	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	77.8168	146	508	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:06,152] [INFO] GTDB search result was written to OceanDNA-a1881/result_gtdb.tsv
[2023-03-15 22:45:06,157] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:06,162] [INFO] DFAST_QC result json was written to OceanDNA-a1881/dqc_result.json
[2023-03-15 22:45:06,162] [INFO] DFAST_QC completed!
[2023-03-15 22:45:06,162] [INFO] Total running time: 0h0m44s