[2023-03-17 23:08:31,911] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference
[2023-03-17 23:08:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,079] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,079] [INFO] Running command: cat /var/lib/cwl/stgcdd6ab8a-16ce-4343-85c4-1b52eb4220c4/OceanDNA-b16243.fa | prodigal -d OceanDNA-b16243/cds.fna -a OceanDNA-b16243/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:49,972] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:49,973] [INFO] Task started: HMMsearch
[2023-03-17 23:08:49,973] [INFO] Running command: hmmsearch --tblout OceanDNA-b16243/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/reference_markers.hmm OceanDNA-b16243/protein.faa > /dev/null
[2023-03-17 23:08:50,165] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:50,166] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcdd6ab8a-16ce-4343-85c4-1b52eb4220c4/OceanDNA-b16243.fa]
[2023-03-17 23:08:50,181] [INFO] Query marker FASTA was written to OceanDNA-b16243/markers.fasta
[2023-03-17 23:08:50,182] [INFO] Task started: Blastn
[2023-03-17 23:08:50,182] [INFO] Running command: blastn -query OceanDNA-b16243/markers.fasta -db /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/reference_markers.fasta -out OceanDNA-b16243/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:50,723] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:50,729] [INFO] Selected 23 target genomes.
[2023-03-17 23:08:50,729] [INFO] Target genome list was writen to OceanDNA-b16243/target_genomes.txt
[2023-03-17 23:08:50,739] [INFO] Task started: fastANI
[2023-03-17 23:08:50,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdd6ab8a-16ce-4343-85c4-1b52eb4220c4/OceanDNA-b16243.fa --refList OceanDNA-b16243/target_genomes.txt --output OceanDNA-b16243/fastani_result.tsv --threads 1
[2023-03-17 23:09:04,296] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:04,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:04,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:04,300] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:04,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:09:04,301] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.7564	180	625	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.8898	97	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:09:04,301] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16243/tc_result.tsv
[2023-03-17 23:09:04,301] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:04,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:04,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/checkm_data
[2023-03-17 23:09:04,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:04,318] [INFO] Task started: CheckM
[2023-03-17 23:09:04,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16243/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16243/checkm_input OceanDNA-b16243/checkm_result
[2023-03-17 23:09:48,555] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:48,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:48,590] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:48,590] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:48,591] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16243/markers.fasta)
[2023-03-17 23:09:48,592] [INFO] Task started: Blastn
[2023-03-17 23:09:48,592] [INFO] Running command: blastn -query OceanDNA-b16243/markers.fasta -db /var/lib/cwl/stgba34cf7b-38a0-400a-b7e7-65cc2406d844/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16243/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:49,457] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:49,461] [INFO] Selected 12 target genomes.
[2023-03-17 23:09:49,461] [INFO] Target genome list was writen to OceanDNA-b16243/target_genomes_gtdb.txt
[2023-03-17 23:09:49,473] [INFO] Task started: fastANI
[2023-03-17 23:09:49,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdd6ab8a-16ce-4343-85c4-1b52eb4220c4/OceanDNA-b16243.fa --refList OceanDNA-b16243/target_genomes_gtdb.txt --output OceanDNA-b16243/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:55,579] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:55,586] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:09:55,586] [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_002737305.1	s__BAIKAL-G1 sp002737305	98.226	404	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016463595.1	s__BAIKAL-G1 sp016463595	93.3967	495	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903855705.1	s__BAIKAL-G1 sp903855705	89.1691	506	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	98.86	98.32	0.88	0.87	5	-
GCF_002252705.1	s__Vulcanococcus limneticus	80.9523	444	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003925.1	s__Cyanobium minutissimum	80.2598	386	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCF_002252675.1	s__Cyanobium sp002252675	80.2543	392	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCA_010030955.1	s__Vulcanococcus sp010030955	80.0988	298	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.81	98.81	0.81	0.81	2	-
GCA_016882315.1	s__Cyanobium sp016882315	80.006	386	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934375.1	s__Vulcanococcus sp903934375	79.7772	339	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
GCF_000179235.2	s__Vulcanococcus sp000179235	79.7732	360	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088535.1	s__NIES-981 sp900088535	79.4292	369	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249115.1	s__QBMD01 sp003249115	79.1723	302	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:55,590] [INFO] GTDB search result was written to OceanDNA-b16243/result_gtdb.tsv
[2023-03-17 23:09:55,592] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:55,595] [INFO] DFAST_QC result json was written to OceanDNA-b16243/dqc_result.json
[2023-03-17 23:09:55,595] [INFO] DFAST_QC completed!
[2023-03-17 23:09:55,595] [INFO] Total running time: 0h1m24s