[2023-03-18 07:29:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg9fa28b75-50e3-4268-a9fb-600c34fe8b9c/OceanDNA-a2213.fa | prodigal -d OceanDNA-a2213/cds.fna -a OceanDNA-a2213/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:40,371] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:40,371] [INFO] Task started: HMMsearch
[2023-03-18 07:29:40,371] [INFO] Running command: hmmsearch --tblout OceanDNA-a2213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/reference_markers.hmm OceanDNA-a2213/protein.faa > /dev/null
[2023-03-18 07:29:40,527] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:40,527] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9fa28b75-50e3-4268-a9fb-600c34fe8b9c/OceanDNA-a2213.fa]
[2023-03-18 07:29:40,538] [INFO] Query marker FASTA was written to OceanDNA-a2213/markers.fasta
[2023-03-18 07:29:40,538] [INFO] Task started: Blastn
[2023-03-18 07:29:40,539] [INFO] Running command: blastn -query OceanDNA-a2213/markers.fasta -db /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/reference_markers.fasta -out OceanDNA-a2213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:40,999] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:40,999] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:40,999] [INFO] Target genome list was writen to OceanDNA-a2213/target_genomes.txt
[2023-03-18 07:29:41,003] [INFO] Task started: fastANI
[2023-03-18 07:29:41,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fa28b75-50e3-4268-a9fb-600c34fe8b9c/OceanDNA-a2213.fa --refList OceanDNA-a2213/target_genomes.txt --output OceanDNA-a2213/fastani_result.tsv --threads 1
[2023-03-18 07:29:44,078] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:44,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:44,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:44,078] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:44,079] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:44,079] [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
--------------------------------------------------------------------------------
[2023-03-18 07:29:44,079] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2213/tc_result.tsv
[2023-03-18 07:29:44,079] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:44,079] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:44,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/checkm_data
[2023-03-18 07:29:44,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:44,084] [INFO] Task started: CheckM
[2023-03-18 07:29:44,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2213/checkm_input OceanDNA-a2213/checkm_result
[2023-03-18 07:30:11,031] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:11,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:11,033] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:11,033] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:11,033] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2213/markers.fasta)
[2023-03-18 07:30:11,033] [INFO] Task started: Blastn
[2023-03-18 07:30:11,033] [INFO] Running command: blastn -query OceanDNA-a2213/markers.fasta -db /var/lib/cwl/stg13e708f7-c60b-4db9-a145-c77f28676685/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:11,584] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:11,585] [INFO] Selected 10 target genomes.
[2023-03-18 07:30:11,585] [INFO] Target genome list was writen to OceanDNA-a2213/target_genomes_gtdb.txt
[2023-03-18 07:30:11,777] [INFO] Task started: fastANI
[2023-03-18 07:30:11,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fa28b75-50e3-4268-a9fb-600c34fe8b9c/OceanDNA-a2213.fa --refList OceanDNA-a2213/target_genomes_gtdb.txt --output OceanDNA-a2213/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:14,890] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:14,895] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:14,896] [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_013329255.1	s__MGIIa-L1 sp9513u	79.4017	234	418	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_905181785.1	s__MGIIa-L1 sp905181785	79.3797	222	418	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_002502605.1	s__MGIIa-L1 sp002502605	78.732	155	418	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.35	99.06	0.87	0.87	3	-
GCA_000246735.1	s__MGIIa-L1 sp000246735	77.9046	161	418	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	-
GCA_905182125.1	s__MGIIa-L1 sp905182125	77.885	164	418	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_009887095.1	s__MGIIa-L1 sp009887095	77.5457	136	418	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_013330285.1	s__MGIIa-L1 sp8160u	77.3794	117	418	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	97.88	96.83	0.79	0.69	4	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:14,896] [INFO] GTDB search result was written to OceanDNA-a2213/result_gtdb.tsv
[2023-03-18 07:30:14,896] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:14,897] [INFO] DFAST_QC result json was written to OceanDNA-a2213/dqc_result.json
[2023-03-18 07:30:14,897] [INFO] DFAST_QC completed!
[2023-03-18 07:30:14,897] [INFO] Total running time: 0h0m45s