[2023-03-16 09:15:41,451] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:15:41,451] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:15:41,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference
[2023-03-16 09:15:42,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:15:42,558] [INFO] Task started: Prodigal
[2023-03-16 09:15:42,559] [INFO] Running command: cat /var/lib/cwl/stgf5589912-09d2-4c25-bd7e-d82d806dc68a/OceanDNA-a1596.fa | prodigal -d OceanDNA-a1596/cds.fna -a OceanDNA-a1596/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:15:45,189] [INFO] Task succeeded: Prodigal
[2023-03-16 09:15:45,190] [INFO] Task started: HMMsearch
[2023-03-16 09:15:45,190] [INFO] Running command: hmmsearch --tblout OceanDNA-a1596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/reference_markers.hmm OceanDNA-a1596/protein.faa > /dev/null
[2023-03-16 09:15:45,322] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:15:45,322] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf5589912-09d2-4c25-bd7e-d82d806dc68a/OceanDNA-a1596.fa]
[2023-03-16 09:15:45,329] [INFO] Query marker FASTA was written to OceanDNA-a1596/markers.fasta
[2023-03-16 09:15:45,331] [INFO] Task started: Blastn
[2023-03-16 09:15:45,331] [INFO] Running command: blastn -query OceanDNA-a1596/markers.fasta -db /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/reference_markers.fasta -out OceanDNA-a1596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:15:45,845] [INFO] Task succeeded: Blastn
[2023-03-16 09:15:45,846] [INFO] Selected 5 target genomes.
[2023-03-16 09:15:45,846] [INFO] Target genome list was writen to OceanDNA-a1596/target_genomes.txt
[2023-03-16 09:15:45,851] [INFO] Task started: fastANI
[2023-03-16 09:15:45,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5589912-09d2-4c25-bd7e-d82d806dc68a/OceanDNA-a1596.fa --refList OceanDNA-a1596/target_genomes.txt --output OceanDNA-a1596/fastani_result.tsv --threads 1
[2023-03-16 09:15:48,682] [INFO] Task succeeded: fastANI
[2023-03-16 09:15:48,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:15:48,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:15:48,683] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:15:48,683] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:15:48,683] [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
--------------------------------------------------------------------------------
[2023-03-16 09:15:48,683] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1596/tc_result.tsv
[2023-03-16 09:15:48,683] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:15:48,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:15:48,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/checkm_data
[2023-03-16 09:15:48,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:15:48,697] [INFO] Task started: CheckM
[2023-03-16 09:15:48,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1596/checkm_input OceanDNA-a1596/checkm_result
[2023-03-16 09:16:03,828] [INFO] Task succeeded: CheckM
[2023-03-16 09:16:03,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 1.42%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 09:16:03,830] [INFO] ===== Completeness check finished =====
[2023-03-16 09:16:03,830] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:16:03,830] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1596/markers.fasta)
[2023-03-16 09:16:03,832] [INFO] Task started: Blastn
[2023-03-16 09:16:03,832] [INFO] Running command: blastn -query OceanDNA-a1596/markers.fasta -db /var/lib/cwl/stg6533cc17-8f38-423c-ad0b-e8c5101d48d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:16:04,719] [INFO] Task succeeded: Blastn
[2023-03-16 09:16:04,720] [INFO] Selected 6 target genomes.
[2023-03-16 09:16:04,720] [INFO] Target genome list was writen to OceanDNA-a1596/target_genomes_gtdb.txt
[2023-03-16 09:16:04,726] [INFO] Task started: fastANI
[2023-03-16 09:16:04,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5589912-09d2-4c25-bd7e-d82d806dc68a/OceanDNA-a1596.fa --refList OceanDNA-a1596/target_genomes_gtdb.txt --output OceanDNA-a1596/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:16:05,797] [INFO] Task succeeded: fastANI
[2023-03-16 09:16:05,802] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:16:05,802] [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_002497685.1	s__CG-Epi1 sp002497685	83.972	96	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.79	99.79	0.70	0.70	2	-
GCA_001875345.1	s__CG-Epi1 sp001875345	83.0536	115	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	82.8171	113	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718915.1	s__CG-Epi1 sp002718915	82.4761	87	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875365.1	s__CG-Epi1 sp001875365	81.6772	65	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724775.1	s__CG-Epi1 sp002724775	80.4074	102	146	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	96.65	95.92	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-16 09:16:05,802] [INFO] GTDB search result was written to OceanDNA-a1596/result_gtdb.tsv
[2023-03-16 09:16:05,802] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:16:05,803] [INFO] DFAST_QC result json was written to OceanDNA-a1596/dqc_result.json
[2023-03-16 09:16:05,803] [INFO] DFAST_QC completed!
[2023-03-16 09:16:05,803] [INFO] Total running time: 0h0m24s