[2023-03-18 01:35:16,890] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:35:16,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:35:16,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg517099fe-3ac9-48af-bce6-428f4a354dcf/dqc_reference
[2023-03-18 01:35:18,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:35:18,358] [INFO] Task started: Prodigal
[2023-03-18 01:35:18,358] [INFO] Running command: cat /var/lib/cwl/stg3c8ba42d-d2e1-4cef-8752-e9f3da566ee9/OceanDNA-a1886.fa | prodigal -d OceanDNA-a1886/cds.fna -a OceanDNA-a1886/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:35:24,836] [INFO] Task succeeded: Prodigal
[2023-03-18 01:35:24,837] [INFO] Task started: HMMsearch
[2023-03-18 01:35:24,837] [INFO] Running command: hmmsearch --tblout OceanDNA-a1886/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg517099fe-3ac9-48af-bce6-428f4a354dcf/dqc_reference/reference_markers.hmm OceanDNA-a1886/protein.faa > /dev/null
[2023-03-18 01:35:24,983] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:35:24,984] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3c8ba42d-d2e1-4cef-8752-e9f3da566ee9/OceanDNA-a1886.fa]
[2023-03-18 01:35:24,999] [INFO] Query marker FASTA was written to OceanDNA-a1886/markers.fasta
[2023-03-18 01:35:24,999] [INFO] Task started: Blastn
[2023-03-18 01:35:24,999] [INFO] Running command: blastn -query OceanDNA-a1886/markers.fasta -db /var/lib/cwl/stg517099fe-3ac9-48af-bce6-428f4a354dcf/dqc_reference/reference_markers.fasta -out OceanDNA-a1886/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:25,930] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:25,930] [INFO] Selected 0 target genomes.
[2023-03-18 01:35:25,931] [INFO] Target genome list was writen to OceanDNA-a1886/target_genomes.txt
[2023-03-18 01:35:25,931] [ERROR] File is empty. [OceanDNA-a1886/target_genomes.txt]
[2023-03-18 01:35:25,931] [ERROR] Task failed. No target genome found.
[2023-03-18 01:35:25,931] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:35:25,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg517099fe-3ac9-48af-bce6-428f4a354dcf/dqc_reference/checkm_data
[2023-03-18 01:35:25,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:35:25,938] [INFO] Task started: CheckM
[2023-03-18 01:35:25,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1886/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1886/checkm_input OceanDNA-a1886/checkm_result
[2023-03-18 01:35:47,688] [INFO] Task succeeded: CheckM
[2023-03-18 01:35:47,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:35:47,694] [INFO] ===== Completeness check finished =====
[2023-03-18 01:35:47,694] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:35:47,695] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1886/markers.fasta)
[2023-03-18 01:35:47,696] [INFO] Task started: Blastn
[2023-03-18 01:35:47,696] [INFO] Running command: blastn -query OceanDNA-a1886/markers.fasta -db /var/lib/cwl/stg517099fe-3ac9-48af-bce6-428f4a354dcf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1886/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:48,306] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:48,309] [INFO] Selected 11 target genomes.
[2023-03-18 01:35:48,309] [INFO] Target genome list was writen to OceanDNA-a1886/target_genomes_gtdb.txt
[2023-03-18 01:35:48,313] [INFO] Task started: fastANI
[2023-03-18 01:35:48,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8ba42d-d2e1-4cef-8752-e9f3da566ee9/OceanDNA-a1886.fa --refList OceanDNA-a1886/target_genomes_gtdb.txt --output OceanDNA-a1886/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:35:51,466] [INFO] Task succeeded: fastANI
[2023-03-18 01:35:51,472] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:35:51,472] [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_002689565.1	s__MGIIa-K1 sp002689565	97.8272	190	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002710205.1	s__MGIIa-K1 sp002710205	78.7177	123	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709705.1	s__MGIIa-K1 sp002709705	78.4586	128	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	78.1848	134	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	78.1703	120	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	78.044	131	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701145.1	s__MGIIa-K1 sp002701145	76.9435	81	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	76.6797	92	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:35:51,474] [INFO] GTDB search result was written to OceanDNA-a1886/result_gtdb.tsv
[2023-03-18 01:35:51,475] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:35:51,476] [INFO] DFAST_QC result json was written to OceanDNA-a1886/dqc_result.json
[2023-03-18 01:35:51,476] [INFO] DFAST_QC completed!
[2023-03-18 01:35:51,476] [INFO] Total running time: 0h0m35s