[2023-03-15 06:28:21,425] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,425] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference
[2023-03-15 06:28:22,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,548] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,548] [INFO] Running command: cat /var/lib/cwl/stg2388f3bb-edfb-4d2e-9392-6609d4a46e58/OceanDNA-a4456.fa | prodigal -d OceanDNA-a4456/cds.fna -a OceanDNA-a4456/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:31,802] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:31,802] [INFO] Task started: HMMsearch
[2023-03-15 06:28:31,802] [INFO] Running command: hmmsearch --tblout OceanDNA-a4456/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/reference_markers.hmm OceanDNA-a4456/protein.faa > /dev/null
[2023-03-15 06:28:31,953] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:31,954] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2388f3bb-edfb-4d2e-9392-6609d4a46e58/OceanDNA-a4456.fa]
[2023-03-15 06:28:31,963] [INFO] Query marker FASTA was written to OceanDNA-a4456/markers.fasta
[2023-03-15 06:28:31,963] [INFO] Task started: Blastn
[2023-03-15 06:28:31,964] [INFO] Running command: blastn -query OceanDNA-a4456/markers.fasta -db /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/reference_markers.fasta -out OceanDNA-a4456/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:32,398] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:32,399] [INFO] Selected 3 target genomes.
[2023-03-15 06:28:32,399] [INFO] Target genome list was writen to OceanDNA-a4456/target_genomes.txt
[2023-03-15 06:28:32,401] [INFO] Task started: fastANI
[2023-03-15 06:28:32,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg2388f3bb-edfb-4d2e-9392-6609d4a46e58/OceanDNA-a4456.fa --refList OceanDNA-a4456/target_genomes.txt --output OceanDNA-a4456/fastani_result.tsv --threads 1
[2023-03-15 06:28:33,523] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:33,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:33,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:33,524] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:33,524] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:33,524] [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
--------------------------------------------------------------------------------
[2023-03-15 06:28:33,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4456/tc_result.tsv
[2023-03-15 06:28:33,544] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:33,544] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:33,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/checkm_data
[2023-03-15 06:28:33,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:33,608] [INFO] Task started: CheckM
[2023-03-15 06:28:33,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4456/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4456/checkm_input OceanDNA-a4456/checkm_result
[2023-03-15 06:29:02,224] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:02,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.20%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:02,226] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:02,226] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:02,226] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4456/markers.fasta)
[2023-03-15 06:29:02,227] [INFO] Task started: Blastn
[2023-03-15 06:29:02,227] [INFO] Running command: blastn -query OceanDNA-a4456/markers.fasta -db /var/lib/cwl/stg85514ac7-2132-4d47-801b-65a881604071/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4456/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:02,617] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:02,625] [INFO] Selected 10 target genomes.
[2023-03-15 06:29:02,625] [INFO] Target genome list was writen to OceanDNA-a4456/target_genomes_gtdb.txt
[2023-03-15 06:29:02,629] [INFO] Task started: fastANI
[2023-03-15 06:29:02,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg2388f3bb-edfb-4d2e-9392-6609d4a46e58/OceanDNA-a4456.fa --refList OceanDNA-a4456/target_genomes_gtdb.txt --output OceanDNA-a4456/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:05,020] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:05,024] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:05,025] [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_002505775.1	s__MGIIb-O5 sp002505775	89.6983	337	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.25	97.62	0.92	0.83	5	-
GCA_002501605.1	s__MGIIb-O5 sp002501605	88.705	307	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.05	98.72	0.89	0.86	6	-
GCA_002730095.1	s__MGIIb-O5 sp002730095	79.5106	192	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.71	97.66	0.85	0.80	5	-
GCA_002501805.1	s__MGIIb-O5 sp002501805	78.2714	123	376	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	78.1264	116	376	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_002496725.1	s__MGIIb-O5 sp002496725	76.6736	87	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.85	99.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:05,025] [INFO] GTDB search result was written to OceanDNA-a4456/result_gtdb.tsv
[2023-03-15 06:29:05,025] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:05,025] [INFO] DFAST_QC result json was written to OceanDNA-a4456/dqc_result.json
[2023-03-15 06:29:05,026] [INFO] DFAST_QC completed!
[2023-03-15 06:29:05,026] [INFO] Total running time: 0h0m44s