[2023-03-19 02:10:16,859] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:10:16,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:10:16,859] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference
[2023-03-19 02:10:18,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:10:18,814] [INFO] Task started: Prodigal
[2023-03-19 02:10:18,814] [INFO] Running command: cat /var/lib/cwl/stgd4ec3ae5-f3fa-4ce0-bd87-07e4a737cb2e/OceanDNA-a2385.fa | prodigal -d OceanDNA-a2385/cds.fna -a OceanDNA-a2385/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:10:24,882] [INFO] Task succeeded: Prodigal
[2023-03-19 02:10:24,882] [INFO] Task started: HMMsearch
[2023-03-19 02:10:24,882] [INFO] Running command: hmmsearch --tblout OceanDNA-a2385/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/reference_markers.hmm OceanDNA-a2385/protein.faa > /dev/null
[2023-03-19 02:10:25,034] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:10:25,034] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd4ec3ae5-f3fa-4ce0-bd87-07e4a737cb2e/OceanDNA-a2385.fa]
[2023-03-19 02:10:25,047] [INFO] Query marker FASTA was written to OceanDNA-a2385/markers.fasta
[2023-03-19 02:10:25,048] [INFO] Task started: Blastn
[2023-03-19 02:10:25,048] [INFO] Running command: blastn -query OceanDNA-a2385/markers.fasta -db /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/reference_markers.fasta -out OceanDNA-a2385/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:25,468] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:25,468] [INFO] Selected 3 target genomes.
[2023-03-19 02:10:25,469] [INFO] Target genome list was writen to OceanDNA-a2385/target_genomes.txt
[2023-03-19 02:10:25,470] [INFO] Task started: fastANI
[2023-03-19 02:10:25,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ec3ae5-f3fa-4ce0-bd87-07e4a737cb2e/OceanDNA-a2385.fa --refList OceanDNA-a2385/target_genomes.txt --output OceanDNA-a2385/fastani_result.tsv --threads 1
[2023-03-19 02:10:27,634] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:27,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:10:27,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:10:27,635] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:10:27,635] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:10:27,635] [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 02:10:27,635] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2385/tc_result.tsv
[2023-03-19 02:10:27,635] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:10:27,635] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:10:27,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/checkm_data
[2023-03-19 02:10:27,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:10:27,978] [INFO] Task started: CheckM
[2023-03-19 02:10:27,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2385/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2385/checkm_input OceanDNA-a2385/checkm_result
[2023-03-19 02:10:52,672] [INFO] Task succeeded: CheckM
[2023-03-19 02:10:52,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.99%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:10:52,675] [INFO] ===== Completeness check finished =====
[2023-03-19 02:10:52,675] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:10:52,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2385/markers.fasta)
[2023-03-19 02:10:52,677] [INFO] Task started: Blastn
[2023-03-19 02:10:52,677] [INFO] Running command: blastn -query OceanDNA-a2385/markers.fasta -db /var/lib/cwl/stgf5b0cd23-578d-4338-bcba-946d1c808377/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2385/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:53,517] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:53,519] [INFO] Selected 11 target genomes.
[2023-03-19 02:10:53,520] [INFO] Target genome list was writen to OceanDNA-a2385/target_genomes_gtdb.txt
[2023-03-19 02:10:53,606] [INFO] Task started: fastANI
[2023-03-19 02:10:53,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ec3ae5-f3fa-4ce0-bd87-07e4a737cb2e/OceanDNA-a2385.fa --refList OceanDNA-a2385/target_genomes_gtdb.txt --output OceanDNA-a2385/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:10:56,770] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:56,775] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:10:56,775] [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_002170315.2	s__MGIIa-L1 sp002170315	94.6746	211	240	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_002499705.1	s__MGIIa-L1 sp002499705	83.9583	207	240	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_902520595.1	s__MGIIa-L1 sp902520595	82.6877	135	240	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_009937025.1	s__MGIIa-L1 sp009937025	79.315	126	240	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_018662825.1	s__MGIIa-L1 sp018662825	78.6668	126	240	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_905182725.1	s__MGIIa-L1 sp905182725	78.374	113	240	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_905182635.1	s__MGIIa-L1 sp905182635	78.0268	80	240	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_002687075.1	s__MGIIa-L1 sp002687075	77.4758	83	240	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-19 02:10:56,776] [INFO] GTDB search result was written to OceanDNA-a2385/result_gtdb.tsv
[2023-03-19 02:10:56,776] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:10:56,777] [INFO] DFAST_QC result json was written to OceanDNA-a2385/dqc_result.json
[2023-03-19 02:10:56,777] [INFO] DFAST_QC completed!
[2023-03-19 02:10:56,777] [INFO] Total running time: 0h0m40s