[2023-03-15 11:24:11,467] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference
[2023-03-15 11:24:12,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,589] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,589] [INFO] Running command: cat /var/lib/cwl/stgfc20d21a-1694-4482-bfd6-e99e08e7e642/OceanDNA-a2828.fa | prodigal -d OceanDNA-a2828/cds.fna -a OceanDNA-a2828/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:24,665] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:24,665] [INFO] Task started: HMMsearch
[2023-03-15 11:24:24,665] [INFO] Running command: hmmsearch --tblout OceanDNA-a2828/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/reference_markers.hmm OceanDNA-a2828/protein.faa > /dev/null
[2023-03-15 11:24:24,832] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:24,833] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfc20d21a-1694-4482-bfd6-e99e08e7e642/OceanDNA-a2828.fa]
[2023-03-15 11:24:24,846] [INFO] Query marker FASTA was written to OceanDNA-a2828/markers.fasta
[2023-03-15 11:24:24,846] [INFO] Task started: Blastn
[2023-03-15 11:24:24,846] [INFO] Running command: blastn -query OceanDNA-a2828/markers.fasta -db /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/reference_markers.fasta -out OceanDNA-a2828/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:25,275] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:25,275] [INFO] Selected 5 target genomes.
[2023-03-15 11:24:25,276] [INFO] Target genome list was writen to OceanDNA-a2828/target_genomes.txt
[2023-03-15 11:24:25,279] [INFO] Task started: fastANI
[2023-03-15 11:24:25,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc20d21a-1694-4482-bfd6-e99e08e7e642/OceanDNA-a2828.fa --refList OceanDNA-a2828/target_genomes.txt --output OceanDNA-a2828/fastani_result.tsv --threads 1
[2023-03-15 11:24:28,079] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:28,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:28,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:28,080] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:28,080] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:24:28,080] [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
--------------------------------------------------------------------------------
[2023-03-15 11:24:28,080] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2828/tc_result.tsv
[2023-03-15 11:24:28,080] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:28,080] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:28,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/checkm_data
[2023-03-15 11:24:28,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:28,144] [INFO] Task started: CheckM
[2023-03-15 11:24:28,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2828/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2828/checkm_input OceanDNA-a2828/checkm_result
[2023-03-15 11:25:04,116] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:04,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:04,119] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:04,119] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:04,119] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2828/markers.fasta)
[2023-03-15 11:25:04,120] [INFO] Task started: Blastn
[2023-03-15 11:25:04,120] [INFO] Running command: blastn -query OceanDNA-a2828/markers.fasta -db /var/lib/cwl/stgf571e5ca-4b84-46f5-ae77-49680adb69c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2828/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:04,555] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:04,556] [INFO] Selected 11 target genomes.
[2023-03-15 11:25:04,556] [INFO] Target genome list was writen to OceanDNA-a2828/target_genomes_gtdb.txt
[2023-03-15 11:25:04,569] [INFO] Task started: fastANI
[2023-03-15 11:25:04,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc20d21a-1694-4482-bfd6-e99e08e7e642/OceanDNA-a2828.fa --refList OceanDNA-a2828/target_genomes_gtdb.txt --output OceanDNA-a2828/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:08,387] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:08,393] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:25:08,393] [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_002499195.1	s__MGIIa-L2 sp002499195	99.8616	553	628	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	conclusive
GCA_002698145.1	s__MGIIa-L2 sp002698145	79.7763	335	628	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_002706065.1	s__MGIIa-L2 sp002706065	79.7058	361	628	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_002502215.1	s__MGIIa-L2 sp002502215	79.702	327	628	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.03	97.17	0.84	0.82	4	-
GCA_002719815.1	s__MGIIa-L2 sp002719815	79.3971	272	628	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	79.3124	247	628	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_013911465.1	s__MGIIa-L2 sp013911465	79.0817	247	628	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	78.9752	167	628	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	78.5978	295	628	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_002726845.1	s__MGIIa-L2 sp002726845	77.9025	165	628	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.43	97.43	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:08,419] [INFO] GTDB search result was written to OceanDNA-a2828/result_gtdb.tsv
[2023-03-15 11:25:08,420] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:08,421] [INFO] DFAST_QC result json was written to OceanDNA-a2828/dqc_result.json
[2023-03-15 11:25:08,421] [INFO] DFAST_QC completed!
[2023-03-15 11:25:08,421] [INFO] Total running time: 0h0m57s