[2023-03-19 03:50:07,846] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference
[2023-03-19 03:50:09,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,607] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,607] [INFO] Running command: cat /var/lib/cwl/stg20eb7f22-5572-4625-9522-18c1f85c4517/OceanDNA-a2719.fa | prodigal -d OceanDNA-a2719/cds.fna -a OceanDNA-a2719/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:17,286] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:17,287] [INFO] Task started: HMMsearch
[2023-03-19 03:50:17,287] [INFO] Running command: hmmsearch --tblout OceanDNA-a2719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/reference_markers.hmm OceanDNA-a2719/protein.faa > /dev/null
[2023-03-19 03:50:17,481] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:17,481] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg20eb7f22-5572-4625-9522-18c1f85c4517/OceanDNA-a2719.fa]
[2023-03-19 03:50:17,494] [INFO] Query marker FASTA was written to OceanDNA-a2719/markers.fasta
[2023-03-19 03:50:17,494] [INFO] Task started: Blastn
[2023-03-19 03:50:17,494] [INFO] Running command: blastn -query OceanDNA-a2719/markers.fasta -db /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/reference_markers.fasta -out OceanDNA-a2719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:17,930] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:17,931] [INFO] Selected 1 target genomes.
[2023-03-19 03:50:17,931] [INFO] Target genome list was writen to OceanDNA-a2719/target_genomes.txt
[2023-03-19 03:50:17,932] [INFO] Task started: fastANI
[2023-03-19 03:50:17,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg20eb7f22-5572-4625-9522-18c1f85c4517/OceanDNA-a2719.fa --refList OceanDNA-a2719/target_genomes.txt --output OceanDNA-a2719/fastani_result.tsv --threads 1
[2023-03-19 03:50:18,841] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:18,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:18,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:18,842] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:18,842] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:18,842] [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 03:50:18,842] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2719/tc_result.tsv
[2023-03-19 03:50:18,842] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:18,843] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:18,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/checkm_data
[2023-03-19 03:50:18,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:18,848] [INFO] Task started: CheckM
[2023-03-19 03:50:18,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2719/checkm_input OceanDNA-a2719/checkm_result
[2023-03-19 03:50:44,619] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:44,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.64%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:44,621] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:44,621] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:44,621] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2719/markers.fasta)
[2023-03-19 03:50:44,622] [INFO] Task started: Blastn
[2023-03-19 03:50:44,622] [INFO] Running command: blastn -query OceanDNA-a2719/markers.fasta -db /var/lib/cwl/stg84d3105c-6680-4306-8469-648bed492820/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:45,058] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:45,059] [INFO] Selected 10 target genomes.
[2023-03-19 03:50:45,059] [INFO] Target genome list was writen to OceanDNA-a2719/target_genomes_gtdb.txt
[2023-03-19 03:50:45,072] [INFO] Task started: fastANI
[2023-03-19 03:50:45,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg20eb7f22-5572-4625-9522-18c1f85c4517/OceanDNA-a2719.fa --refList OceanDNA-a2719/target_genomes_gtdb.txt --output OceanDNA-a2719/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:48,063] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:48,068] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:50:48,069] [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	85.409	252	346	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_002499195.1	s__MGIIa-L2 sp002499195	80.0638	229	346	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_018623995.1	s__MGIIa-L2 sp018623995	79.2662	174	346	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_002706065.1	s__MGIIa-L2 sp002706065	79.1883	165	346	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_002692685.1	s__MGIIa-L2 sp002692685	79.0689	98	346	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	78.8978	117	346	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_002722615.1	s__MGIIa-L2 sp002722615	78.7828	160	346	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_002171315.2	s__MGIIa-L2 sp002171315	77.5339	78	346	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:48,069] [INFO] GTDB search result was written to OceanDNA-a2719/result_gtdb.tsv
[2023-03-19 03:50:48,069] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:48,070] [INFO] DFAST_QC result json was written to OceanDNA-a2719/dqc_result.json
[2023-03-19 03:50:48,070] [INFO] DFAST_QC completed!
[2023-03-19 03:50:48,070] [INFO] Total running time: 0h0m40s