[2023-03-17 05:10:04,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference
[2023-03-17 05:10:05,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:05,973] [INFO] Task started: Prodigal
[2023-03-17 05:10:05,973] [INFO] Running command: cat /var/lib/cwl/stg4c6eb14c-a844-4632-a18f-6981a079c509/OceanDNA-a2501.fa | prodigal -d OceanDNA-a2501/cds.fna -a OceanDNA-a2501/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:14,853] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:14,853] [INFO] Task started: HMMsearch
[2023-03-17 05:10:14,853] [INFO] Running command: hmmsearch --tblout OceanDNA-a2501/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/reference_markers.hmm OceanDNA-a2501/protein.faa > /dev/null
[2023-03-17 05:10:15,020] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:15,021] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4c6eb14c-a844-4632-a18f-6981a079c509/OceanDNA-a2501.fa]
[2023-03-17 05:10:15,033] [INFO] Query marker FASTA was written to OceanDNA-a2501/markers.fasta
[2023-03-17 05:10:15,033] [INFO] Task started: Blastn
[2023-03-17 05:10:15,033] [INFO] Running command: blastn -query OceanDNA-a2501/markers.fasta -db /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/reference_markers.fasta -out OceanDNA-a2501/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:15,458] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:15,459] [INFO] Selected 6 target genomes.
[2023-03-17 05:10:15,459] [INFO] Target genome list was writen to OceanDNA-a2501/target_genomes.txt
[2023-03-17 05:10:15,463] [INFO] Task started: fastANI
[2023-03-17 05:10:15,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c6eb14c-a844-4632-a18f-6981a079c509/OceanDNA-a2501.fa --refList OceanDNA-a2501/target_genomes.txt --output OceanDNA-a2501/fastani_result.tsv --threads 1
[2023-03-17 05:10:17,825] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:17,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:17,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:17,826] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:17,826] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:10:17,826] [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 05:10:17,826] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2501/tc_result.tsv
[2023-03-17 05:10:17,826] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:17,826] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:17,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/checkm_data
[2023-03-17 05:10:17,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:17,835] [INFO] Task started: CheckM
[2023-03-17 05:10:17,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2501/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2501/checkm_input OceanDNA-a2501/checkm_result
[2023-03-17 05:10:45,302] [INFO] Task succeeded: CheckM
[2023-03-17 05:10:45,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:10:45,305] [INFO] ===== Completeness check finished =====
[2023-03-17 05:10:45,305] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:10:45,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2501/markers.fasta)
[2023-03-17 05:10:45,305] [INFO] Task started: Blastn
[2023-03-17 05:10:45,305] [INFO] Running command: blastn -query OceanDNA-a2501/markers.fasta -db /var/lib/cwl/stg0d8ea890-6b03-48c6-a960-f2eb476038f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2501/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:45,736] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:45,737] [INFO] Selected 9 target genomes.
[2023-03-17 05:10:45,737] [INFO] Target genome list was writen to OceanDNA-a2501/target_genomes_gtdb.txt
[2023-03-17 05:10:45,985] [INFO] Task started: fastANI
[2023-03-17 05:10:45,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c6eb14c-a844-4632-a18f-6981a079c509/OceanDNA-a2501.fa --refList OceanDNA-a2501/target_genomes_gtdb.txt --output OceanDNA-a2501/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:10:49,625] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:49,630] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:10:49,630] [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_002172355.2	s__MGIIa-L1 sp002172355	98.7146	398	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.37	98.74	0.95	0.91	3	conclusive
GCA_002697705.1	s__MGIIa-L1 sp002697705	91.0199	384	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.07	99.07	0.77	0.77	2	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	84.5353	475	529	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_018667575.1	s__MGIIa-L1 sp018667575	81.3262	365	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.28	99.11	0.90	0.88	4	-
GCA_002702945.1	s__MGIIa-L1 sp002702945	78.902	259	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
GCA_002729095.1	s__MGIIa-L1 sp002729095	78.4533	205	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.94	98.73	0.83	0.79	6	-
--------------------------------------------------------------------------------
[2023-03-17 05:10:49,630] [INFO] GTDB search result was written to OceanDNA-a2501/result_gtdb.tsv
[2023-03-17 05:10:49,630] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:10:49,631] [INFO] DFAST_QC result json was written to OceanDNA-a2501/dqc_result.json
[2023-03-17 05:10:49,631] [INFO] DFAST_QC completed!
[2023-03-17 05:10:49,631] [INFO] Total running time: 0h0m45s