[2023-03-18 22:54:22,107] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:54:22,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:54:22,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference
[2023-03-18 22:54:23,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:54:23,185] [INFO] Task started: Prodigal
[2023-03-18 22:54:23,186] [INFO] Running command: cat /var/lib/cwl/stgf65f2aec-c0e8-468b-bef4-0119758a7fc4/OceanDNA-a4561.fa | prodigal -d OceanDNA-a4561/cds.fna -a OceanDNA-a4561/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:54:29,859] [INFO] Task succeeded: Prodigal
[2023-03-18 22:54:29,859] [INFO] Task started: HMMsearch
[2023-03-18 22:54:29,859] [INFO] Running command: hmmsearch --tblout OceanDNA-a4561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/reference_markers.hmm OceanDNA-a4561/protein.faa > /dev/null
[2023-03-18 22:54:30,008] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:54:30,009] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf65f2aec-c0e8-468b-bef4-0119758a7fc4/OceanDNA-a4561.fa]
[2023-03-18 22:54:30,019] [INFO] Query marker FASTA was written to OceanDNA-a4561/markers.fasta
[2023-03-18 22:54:30,020] [INFO] Task started: Blastn
[2023-03-18 22:54:30,021] [INFO] Running command: blastn -query OceanDNA-a4561/markers.fasta -db /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/reference_markers.fasta -out OceanDNA-a4561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:30,447] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:30,448] [INFO] Selected 5 target genomes.
[2023-03-18 22:54:30,448] [INFO] Target genome list was writen to OceanDNA-a4561/target_genomes.txt
[2023-03-18 22:54:30,452] [INFO] Task started: fastANI
[2023-03-18 22:54:30,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgf65f2aec-c0e8-468b-bef4-0119758a7fc4/OceanDNA-a4561.fa --refList OceanDNA-a4561/target_genomes.txt --output OceanDNA-a4561/fastani_result.tsv --threads 1
[2023-03-18 22:54:32,887] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:32,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:54:32,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:54:32,888] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:54:32,888] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:54:32,888] [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 22:54:32,888] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4561/tc_result.tsv
[2023-03-18 22:54:32,888] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:54:32,889] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:54:32,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/checkm_data
[2023-03-18 22:54:32,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:54:32,894] [INFO] Task started: CheckM
[2023-03-18 22:54:32,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4561/checkm_input OceanDNA-a4561/checkm_result
[2023-03-18 22:54:55,431] [INFO] Task succeeded: CheckM
[2023-03-18 22:54:55,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:54:55,437] [INFO] ===== Completeness check finished =====
[2023-03-18 22:54:55,437] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:54:55,437] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4561/markers.fasta)
[2023-03-18 22:54:55,438] [INFO] Task started: Blastn
[2023-03-18 22:54:55,438] [INFO] Running command: blastn -query OceanDNA-a4561/markers.fasta -db /var/lib/cwl/stgcfbdcda6-1c05-4edb-b865-bca84ea5b68c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:55,863] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:55,864] [INFO] Selected 8 target genomes.
[2023-03-18 22:54:55,864] [INFO] Target genome list was writen to OceanDNA-a4561/target_genomes_gtdb.txt
[2023-03-18 22:54:55,869] [INFO] Task started: fastANI
[2023-03-18 22:54:55,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgf65f2aec-c0e8-468b-bef4-0119758a7fc4/OceanDNA-a4561.fa --refList OceanDNA-a4561/target_genomes_gtdb.txt --output OceanDNA-a4561/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:54:57,947] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:57,951] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:54:57,951] [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_002506825.1	s__MGIIb-O5 sp002506825	90.0916	326	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.02	97.97	0.86	0.84	3	-
GCA_002499865.1	s__MGIIb-O5 sp002499865	81.2068	250	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.65	99.57	0.89	0.88	3	-
GCA_002501805.1	s__MGIIb-O5 sp002501805	81.1046	262	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	97.49	96.31	0.90	0.85	5	-
GCA_002502095.1	s__MGIIb-O5 sp002502095	80.9769	263	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.50	98.52	0.89	0.78	6	-
GCA_002499325.1	s__MGIIb-O5 sp002499325	79.8012	213	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.30	99.30	0.84	0.84	2	-
GCA_002496725.1	s__MGIIb-O5 sp002496725	78.2471	153	381	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.85	99.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:54:57,952] [INFO] GTDB search result was written to OceanDNA-a4561/result_gtdb.tsv
[2023-03-18 22:54:57,954] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:54:57,955] [INFO] DFAST_QC result json was written to OceanDNA-a4561/dqc_result.json
[2023-03-18 22:54:57,955] [INFO] DFAST_QC completed!
[2023-03-18 22:54:57,955] [INFO] Total running time: 0h0m36s