[2023-03-18 01:33:52,426] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:33:52,426] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:33:52,426] [INFO] DQC Reference Directory: /var/lib/cwl/stgdba0c037-105a-4479-b52d-8e43273aa145/dqc_reference
[2023-03-18 01:33:53,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:33:53,572] [INFO] Task started: Prodigal
[2023-03-18 01:33:53,572] [INFO] Running command: cat /var/lib/cwl/stg11754cba-3817-4725-8a88-b24044eac494/OceanDNA-a1888.fa | prodigal -d OceanDNA-a1888/cds.fna -a OceanDNA-a1888/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:34:00,396] [INFO] Task succeeded: Prodigal
[2023-03-18 01:34:00,397] [INFO] Task started: HMMsearch
[2023-03-18 01:34:00,397] [INFO] Running command: hmmsearch --tblout OceanDNA-a1888/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdba0c037-105a-4479-b52d-8e43273aa145/dqc_reference/reference_markers.hmm OceanDNA-a1888/protein.faa > /dev/null
[2023-03-18 01:34:00,544] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:34:00,544] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg11754cba-3817-4725-8a88-b24044eac494/OceanDNA-a1888.fa]
[2023-03-18 01:34:00,556] [INFO] Query marker FASTA was written to OceanDNA-a1888/markers.fasta
[2023-03-18 01:34:00,557] [INFO] Task started: Blastn
[2023-03-18 01:34:00,557] [INFO] Running command: blastn -query OceanDNA-a1888/markers.fasta -db /var/lib/cwl/stgdba0c037-105a-4479-b52d-8e43273aa145/dqc_reference/reference_markers.fasta -out OceanDNA-a1888/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:34:01,015] [INFO] Task succeeded: Blastn
[2023-03-18 01:34:01,015] [INFO] Selected 0 target genomes.
[2023-03-18 01:34:01,015] [INFO] Target genome list was writen to OceanDNA-a1888/target_genomes.txt
[2023-03-18 01:34:01,016] [ERROR] File is empty. [OceanDNA-a1888/target_genomes.txt]
[2023-03-18 01:34:01,016] [ERROR] Task failed. No target genome found.
[2023-03-18 01:34:01,016] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:34:01,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdba0c037-105a-4479-b52d-8e43273aa145/dqc_reference/checkm_data
[2023-03-18 01:34:01,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:34:01,073] [INFO] Task started: CheckM
[2023-03-18 01:34:01,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1888/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1888/checkm_input OceanDNA-a1888/checkm_result
[2023-03-18 01:34:24,642] [INFO] Task succeeded: CheckM
[2023-03-18 01:34:24,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.86%
Contamintation: 2.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:34:24,644] [INFO] ===== Completeness check finished =====
[2023-03-18 01:34:24,644] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:34:24,645] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1888/markers.fasta)
[2023-03-18 01:34:24,646] [INFO] Task started: Blastn
[2023-03-18 01:34:24,646] [INFO] Running command: blastn -query OceanDNA-a1888/markers.fasta -db /var/lib/cwl/stgdba0c037-105a-4479-b52d-8e43273aa145/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1888/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:34:25,234] [INFO] Task succeeded: Blastn
[2023-03-18 01:34:25,234] [INFO] Selected 10 target genomes.
[2023-03-18 01:34:25,235] [INFO] Target genome list was writen to OceanDNA-a1888/target_genomes_gtdb.txt
[2023-03-18 01:34:25,242] [INFO] Task started: fastANI
[2023-03-18 01:34:25,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg11754cba-3817-4725-8a88-b24044eac494/OceanDNA-a1888.fa --refList OceanDNA-a1888/target_genomes_gtdb.txt --output OceanDNA-a1888/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:34:28,234] [INFO] Task succeeded: fastANI
[2023-03-18 01:34:28,240] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:34:28,240] [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_002506705.1	s__MGIIa-K1 sp002506705	79.9869	134	366	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_011525095.1	s__MGIIa-K1 sp011525095	79.2626	152	366	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_011522915.1	s__MGIIa-K1 sp011522915	78.584	154	366	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	78.4665	131	366	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_002727695.1	s__MGIIa-K1 sp002727695	78.4005	130	366	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_002715725.1	s__MGIIa-K1 sp002715725	77.4091	123	366	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
GCA_002720115.1	s__MGIIa-K1 sp002720115	77.2869	103	366	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_003602415.1	s__MGIIa-K1 sp003602415	77.0896	111	366	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:34:28,240] [INFO] GTDB search result was written to OceanDNA-a1888/result_gtdb.tsv
[2023-03-18 01:34:28,240] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:34:28,241] [INFO] DFAST_QC result json was written to OceanDNA-a1888/dqc_result.json
[2023-03-18 01:34:28,241] [INFO] DFAST_QC completed!
[2023-03-18 01:34:28,241] [INFO] Total running time: 0h0m36s