[2023-03-19 00:51:14,091] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:51:14,091] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:51:14,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference
[2023-03-19 00:51:15,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:51:15,278] [INFO] Task started: Prodigal
[2023-03-19 00:51:15,278] [INFO] Running command: cat /var/lib/cwl/stgd27d29d4-d927-4f19-ada0-4aff4f2a70a2/OceanDNA-a4130.fa | prodigal -d OceanDNA-a4130/cds.fna -a OceanDNA-a4130/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:51:23,063] [INFO] Task succeeded: Prodigal
[2023-03-19 00:51:23,064] [INFO] Task started: HMMsearch
[2023-03-19 00:51:23,064] [INFO] Running command: hmmsearch --tblout OceanDNA-a4130/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/reference_markers.hmm OceanDNA-a4130/protein.faa > /dev/null
[2023-03-19 00:51:23,269] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:51:23,269] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd27d29d4-d927-4f19-ada0-4aff4f2a70a2/OceanDNA-a4130.fa]
[2023-03-19 00:51:23,278] [INFO] Query marker FASTA was written to OceanDNA-a4130/markers.fasta
[2023-03-19 00:51:23,280] [INFO] Task started: Blastn
[2023-03-19 00:51:23,280] [INFO] Running command: blastn -query OceanDNA-a4130/markers.fasta -db /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/reference_markers.fasta -out OceanDNA-a4130/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:51:23,830] [INFO] Task succeeded: Blastn
[2023-03-19 00:51:23,830] [INFO] Selected 3 target genomes.
[2023-03-19 00:51:23,831] [INFO] Target genome list was writen to OceanDNA-a4130/target_genomes.txt
[2023-03-19 00:51:23,834] [INFO] Task started: fastANI
[2023-03-19 00:51:23,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgd27d29d4-d927-4f19-ada0-4aff4f2a70a2/OceanDNA-a4130.fa --refList OceanDNA-a4130/target_genomes.txt --output OceanDNA-a4130/fastani_result.tsv --threads 1
[2023-03-19 00:51:25,300] [INFO] Task succeeded: fastANI
[2023-03-19 00:51:25,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:51:25,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:51:25,301] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:51:25,301] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:51:25,301] [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
--------------------------------------------------------------------------------
[2023-03-19 00:51:25,301] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4130/tc_result.tsv
[2023-03-19 00:51:25,302] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:51:25,302] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:51:25,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/checkm_data
[2023-03-19 00:51:25,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:51:25,555] [INFO] Task started: CheckM
[2023-03-19 00:51:25,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4130/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4130/checkm_input OceanDNA-a4130/checkm_result
[2023-03-19 00:51:50,079] [INFO] Task succeeded: CheckM
[2023-03-19 00:51:50,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:51:50,081] [INFO] ===== Completeness check finished =====
[2023-03-19 00:51:50,081] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:51:50,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4130/markers.fasta)
[2023-03-19 00:51:50,106] [INFO] Task started: Blastn
[2023-03-19 00:51:50,106] [INFO] Running command: blastn -query OceanDNA-a4130/markers.fasta -db /var/lib/cwl/stg64e075ce-f6e9-44ad-98c4-ac16c4e379bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4130/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:51:50,665] [INFO] Task succeeded: Blastn
[2023-03-19 00:51:50,665] [INFO] Selected 7 target genomes.
[2023-03-19 00:51:50,666] [INFO] Target genome list was writen to OceanDNA-a4130/target_genomes_gtdb.txt
[2023-03-19 00:51:50,671] [INFO] Task started: fastANI
[2023-03-19 00:51:50,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgd27d29d4-d927-4f19-ada0-4aff4f2a70a2/OceanDNA-a4130.fa --refList OceanDNA-a4130/target_genomes_gtdb.txt --output OceanDNA-a4130/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:51:52,653] [INFO] Task succeeded: fastANI
[2023-03-19 00:51:52,658] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:51:52,658] [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_902601345.1	s__MGIIb-O3 sp902601345	99.0138	305	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001629235.1	s__MGIIb-O3 sp001629235	93.3605	289	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.45	95.03	0.80	0.68	7	-
GCA_001629255.1	s__MGIIb-O3 sp001629255	93.3293	338	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.42	97.36	0.80	0.70	6	-
GCA_001628485.1	s__MGIIb-O3 sp001628485	92.5468	365	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.15	97.12	0.88	0.79	10	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	91.9734	255	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625325.1	s__MGIIb-O3 sp902625325	90.8573	338	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573085.1	s__MGIIb-O3 sp902573085	88.0352	258	437	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:51:52,659] [INFO] GTDB search result was written to OceanDNA-a4130/result_gtdb.tsv
[2023-03-19 00:51:52,659] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:51:52,659] [INFO] DFAST_QC result json was written to OceanDNA-a4130/dqc_result.json
[2023-03-19 00:51:52,660] [INFO] DFAST_QC completed!
[2023-03-19 00:51:52,660] [INFO] Total running time: 0h0m39s