[2023-03-15 13:03:55,335] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:55,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:55,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference
[2023-03-15 13:03:56,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:56,437] [INFO] Task started: Prodigal
[2023-03-15 13:03:56,437] [INFO] Running command: cat /var/lib/cwl/stg53a031b5-b20a-4301-9934-e6895a2e6a41/OceanDNA-a1999.fa | prodigal -d OceanDNA-a1999/cds.fna -a OceanDNA-a1999/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:04,907] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:04,908] [INFO] Task started: HMMsearch
[2023-03-15 13:04:04,908] [INFO] Running command: hmmsearch --tblout OceanDNA-a1999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/reference_markers.hmm OceanDNA-a1999/protein.faa > /dev/null
[2023-03-15 13:04:05,071] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:05,071] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg53a031b5-b20a-4301-9934-e6895a2e6a41/OceanDNA-a1999.fa]
[2023-03-15 13:04:05,084] [INFO] Query marker FASTA was written to OceanDNA-a1999/markers.fasta
[2023-03-15 13:04:05,084] [INFO] Task started: Blastn
[2023-03-15 13:04:05,084] [INFO] Running command: blastn -query OceanDNA-a1999/markers.fasta -db /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/reference_markers.fasta -out OceanDNA-a1999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:05,566] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:05,567] [INFO] Selected 5 target genomes.
[2023-03-15 13:04:05,567] [INFO] Target genome list was writen to OceanDNA-a1999/target_genomes.txt
[2023-03-15 13:04:05,571] [INFO] Task started: fastANI
[2023-03-15 13:04:05,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg53a031b5-b20a-4301-9934-e6895a2e6a41/OceanDNA-a1999.fa --refList OceanDNA-a1999/target_genomes.txt --output OceanDNA-a1999/fastani_result.tsv --threads 1
[2023-03-15 13:04:06,960] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:06,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:06,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:06,961] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:06,961] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:06,961] [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 13:04:06,961] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1999/tc_result.tsv
[2023-03-15 13:04:06,961] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:06,961] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:06,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/checkm_data
[2023-03-15 13:04:06,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:06,966] [INFO] Task started: CheckM
[2023-03-15 13:04:06,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1999/checkm_input OceanDNA-a1999/checkm_result
[2023-03-15 13:04:33,488] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:33,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:33,490] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:33,491] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:33,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1999/markers.fasta)
[2023-03-15 13:04:33,491] [INFO] Task started: Blastn
[2023-03-15 13:04:33,491] [INFO] Running command: blastn -query OceanDNA-a1999/markers.fasta -db /var/lib/cwl/stg3eb811dd-5dba-4792-ad13-86e718aa4b47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:34,072] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:34,073] [INFO] Selected 10 target genomes.
[2023-03-15 13:04:34,073] [INFO] Target genome list was writen to OceanDNA-a1999/target_genomes_gtdb.txt
[2023-03-15 13:04:34,168] [INFO] Task started: fastANI
[2023-03-15 13:04:34,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg53a031b5-b20a-4301-9934-e6895a2e6a41/OceanDNA-a1999.fa --refList OceanDNA-a1999/target_genomes_gtdb.txt --output OceanDNA-a1999/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:37,038] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:37,042] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:04:37,042] [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_002707335.2	s__MGIIa-K1 sp002707335	99.4422	310	503	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002727515.1	s__MGIIa-K1 sp002727515	93.45	410	503	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_009936765.1	s__MGIIa-K1 sp009936765	76.648	51	503	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	-
GCA_018650165.1	s__MGIIa-K1 sp018650165	76.6023	69	503	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_011525095.1	s__MGIIa-K1 sp011525095	76.3341	63	503	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 13:04:37,042] [INFO] GTDB search result was written to OceanDNA-a1999/result_gtdb.tsv
[2023-03-15 13:04:37,043] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:37,043] [INFO] DFAST_QC result json was written to OceanDNA-a1999/dqc_result.json
[2023-03-15 13:04:37,043] [INFO] DFAST_QC completed!
[2023-03-15 13:04:37,043] [INFO] Total running time: 0h0m42s