[2023-03-18 07:29:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg71690525-eef7-4dc7-8583-0b3180cc9888/OceanDNA-a2864.fa | prodigal -d OceanDNA-a2864/cds.fna -a OceanDNA-a2864/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:40,064] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:40,064] [INFO] Task started: HMMsearch
[2023-03-18 07:29:40,064] [INFO] Running command: hmmsearch --tblout OceanDNA-a2864/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/reference_markers.hmm OceanDNA-a2864/protein.faa > /dev/null
[2023-03-18 07:29:40,228] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:40,228] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg71690525-eef7-4dc7-8583-0b3180cc9888/OceanDNA-a2864.fa]
[2023-03-18 07:29:40,240] [INFO] Query marker FASTA was written to OceanDNA-a2864/markers.fasta
[2023-03-18 07:29:40,241] [INFO] Task started: Blastn
[2023-03-18 07:29:40,241] [INFO] Running command: blastn -query OceanDNA-a2864/markers.fasta -db /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/reference_markers.fasta -out OceanDNA-a2864/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:40,671] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:40,672] [INFO] Selected 3 target genomes.
[2023-03-18 07:29:40,672] [INFO] Target genome list was writen to OceanDNA-a2864/target_genomes.txt
[2023-03-18 07:29:40,674] [INFO] Task started: fastANI
[2023-03-18 07:29:40,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg71690525-eef7-4dc7-8583-0b3180cc9888/OceanDNA-a2864.fa --refList OceanDNA-a2864/target_genomes.txt --output OceanDNA-a2864/fastani_result.tsv --threads 1
[2023-03-18 07:29:42,236] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:42,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:42,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:42,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:42,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:42,237] [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
--------------------------------------------------------------------------------
[2023-03-18 07:29:42,237] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2864/tc_result.tsv
[2023-03-18 07:29:42,237] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:42,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:42,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/checkm_data
[2023-03-18 07:29:42,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:42,243] [INFO] Task started: CheckM
[2023-03-18 07:29:42,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2864/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2864/checkm_input OceanDNA-a2864/checkm_result
[2023-03-18 07:30:08,254] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:08,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:08,256] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:08,257] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:08,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2864/markers.fasta)
[2023-03-18 07:30:08,257] [INFO] Task started: Blastn
[2023-03-18 07:30:08,257] [INFO] Running command: blastn -query OceanDNA-a2864/markers.fasta -db /var/lib/cwl/stg7f509d74-480c-4c2c-8da3-8e5aa76ff4e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2864/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:08,707] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:08,708] [INFO] Selected 12 target genomes.
[2023-03-18 07:30:08,708] [INFO] Target genome list was writen to OceanDNA-a2864/target_genomes_gtdb.txt
[2023-03-18 07:30:08,858] [INFO] Task started: fastANI
[2023-03-18 07:30:08,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg71690525-eef7-4dc7-8583-0b3180cc9888/OceanDNA-a2864.fa --refList OceanDNA-a2864/target_genomes_gtdb.txt --output OceanDNA-a2864/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:12,326] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:12,330] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:30:12,331] [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_002726845.1	s__MGIIa-L2 sp002726845	96.9198	282	398	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.43	97.43	0.74	0.74	2	conclusive
GCA_012270265.1	s__MGIIa-L2 sp012270265	78.2803	122	398	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_002722615.1	s__MGIIa-L2 sp002722615	77.9851	139	398	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_002698145.1	s__MGIIa-L2 sp002698145	77.9294	147	398	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.10	97.13	0.94	0.83	7	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	77.6948	125	398	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_002496635.1	s__MGIIa-L2 sp002496635	76.6947	63	398	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:12,331] [INFO] GTDB search result was written to OceanDNA-a2864/result_gtdb.tsv
[2023-03-18 07:30:12,331] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:12,332] [INFO] DFAST_QC result json was written to OceanDNA-a2864/dqc_result.json
[2023-03-18 07:30:12,332] [INFO] DFAST_QC completed!
[2023-03-18 07:30:12,332] [INFO] Total running time: 0h0m42s