[2023-03-19 01:13:44,443] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,443] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fb916ce-7808-4b24-9210-28faa85ae947/dqc_reference
[2023-03-19 01:13:45,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,580] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,580] [INFO] Running command: cat /var/lib/cwl/stg371af3bc-8e7e-4858-8cc6-3416f5045fc9/OceanDNA-a2716.fa | prodigal -d OceanDNA-a2716/cds.fna -a OceanDNA-a2716/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:51,540] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:51,540] [INFO] Task started: HMMsearch
[2023-03-19 01:13:51,540] [INFO] Running command: hmmsearch --tblout OceanDNA-a2716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fb916ce-7808-4b24-9210-28faa85ae947/dqc_reference/reference_markers.hmm OceanDNA-a2716/protein.faa > /dev/null
[2023-03-19 01:13:51,682] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:51,682] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg371af3bc-8e7e-4858-8cc6-3416f5045fc9/OceanDNA-a2716.fa]
[2023-03-19 01:13:51,694] [INFO] Query marker FASTA was written to OceanDNA-a2716/markers.fasta
[2023-03-19 01:13:51,694] [INFO] Task started: Blastn
[2023-03-19 01:13:51,694] [INFO] Running command: blastn -query OceanDNA-a2716/markers.fasta -db /var/lib/cwl/stg0fb916ce-7808-4b24-9210-28faa85ae947/dqc_reference/reference_markers.fasta -out OceanDNA-a2716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:52,116] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:52,117] [INFO] Selected 0 target genomes.
[2023-03-19 01:13:52,117] [INFO] Target genome list was writen to OceanDNA-a2716/target_genomes.txt
[2023-03-19 01:13:52,117] [ERROR] File is empty. [OceanDNA-a2716/target_genomes.txt]
[2023-03-19 01:13:52,117] [ERROR] Task failed. No target genome found.
[2023-03-19 01:13:52,117] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:52,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fb916ce-7808-4b24-9210-28faa85ae947/dqc_reference/checkm_data
[2023-03-19 01:13:52,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:52,124] [INFO] Task started: CheckM
[2023-03-19 01:13:52,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2716/checkm_input OceanDNA-a2716/checkm_result
[2023-03-19 01:14:13,880] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:13,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:13,882] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:13,882] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:13,883] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2716/markers.fasta)
[2023-03-19 01:14:13,884] [INFO] Task started: Blastn
[2023-03-19 01:14:13,884] [INFO] Running command: blastn -query OceanDNA-a2716/markers.fasta -db /var/lib/cwl/stg0fb916ce-7808-4b24-9210-28faa85ae947/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:14,295] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:14,295] [INFO] Selected 9 target genomes.
[2023-03-19 01:14:14,296] [INFO] Target genome list was writen to OceanDNA-a2716/target_genomes_gtdb.txt
[2023-03-19 01:14:14,305] [INFO] Task started: fastANI
[2023-03-19 01:14:14,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg371af3bc-8e7e-4858-8cc6-3416f5045fc9/OceanDNA-a2716.fa --refList OceanDNA-a2716/target_genomes_gtdb.txt --output OceanDNA-a2716/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:16,882] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:16,887] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:16,887] [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_002719815.1	s__MGIIa-L2 sp002719815	92.6141	184	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270265.1	s__MGIIa-L2 sp012270265	80.1518	110	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	79.5331	115	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330015.1	s__MGIIa-L2 sp8574u	79.5092	88	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002499195.1	s__MGIIa-L2 sp002499195	79.4977	149	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_002722615.1	s__MGIIa-L2 sp002722615	78.7945	116	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	77.5799	52	244	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:16,888] [INFO] GTDB search result was written to OceanDNA-a2716/result_gtdb.tsv
[2023-03-19 01:14:16,889] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:16,889] [INFO] DFAST_QC result json was written to OceanDNA-a2716/dqc_result.json
[2023-03-19 01:14:16,889] [INFO] DFAST_QC completed!
[2023-03-19 01:14:16,889] [INFO] Total running time: 0h0m32s