[2023-03-17 02:49:37,527] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,527] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference
[2023-03-17 02:49:38,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,734] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,734] [INFO] Running command: cat /var/lib/cwl/stgce9b5f6a-bdc0-4876-85c4-eb9328d9342e/OceanDNA-b16552.fa | prodigal -d OceanDNA-b16552/cds.fna -a OceanDNA-b16552/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:50,008] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:50,008] [INFO] Task started: HMMsearch
[2023-03-17 02:49:50,008] [INFO] Running command: hmmsearch --tblout OceanDNA-b16552/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/reference_markers.hmm OceanDNA-b16552/protein.faa > /dev/null
[2023-03-17 02:49:50,200] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:50,201] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgce9b5f6a-bdc0-4876-85c4-eb9328d9342e/OceanDNA-b16552.fa]
[2023-03-17 02:49:50,214] [INFO] Query marker FASTA was written to OceanDNA-b16552/markers.fasta
[2023-03-17 02:49:50,215] [INFO] Task started: Blastn
[2023-03-17 02:49:50,215] [INFO] Running command: blastn -query OceanDNA-b16552/markers.fasta -db /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/reference_markers.fasta -out OceanDNA-b16552/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:50,644] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:50,645] [INFO] Selected 11 target genomes.
[2023-03-17 02:49:50,645] [INFO] Target genome list was writen to OceanDNA-b16552/target_genomes.txt
[2023-03-17 02:49:50,750] [INFO] Task started: fastANI
[2023-03-17 02:49:50,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9b5f6a-bdc0-4876-85c4-eb9328d9342e/OceanDNA-b16552.fa --refList OceanDNA-b16552/target_genomes.txt --output OceanDNA-b16552/fastani_result.tsv --threads 1
[2023-03-17 02:49:57,377] [INFO] Task succeeded: fastANI
[2023-03-17 02:49:57,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:49:57,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:49:57,381] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:49:57,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:49:57,381] [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	78.6499	164	298	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:49:57,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16552/tc_result.tsv
[2023-03-17 02:49:57,381] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:49:57,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:49:57,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/checkm_data
[2023-03-17 02:49:57,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:49:57,385] [INFO] Task started: CheckM
[2023-03-17 02:49:57,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16552/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16552/checkm_input OceanDNA-b16552/checkm_result
[2023-03-17 02:50:31,434] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:31,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:31,453] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:31,453] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:31,454] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16552/markers.fasta)
[2023-03-17 02:50:31,455] [INFO] Task started: Blastn
[2023-03-17 02:50:31,455] [INFO] Running command: blastn -query OceanDNA-b16552/markers.fasta -db /var/lib/cwl/stg8966f9c2-bdb2-412c-8fcb-b2b295d37223/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16552/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:31,887] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:31,891] [INFO] Selected 8 target genomes.
[2023-03-17 02:50:31,891] [INFO] Target genome list was writen to OceanDNA-b16552/target_genomes_gtdb.txt
[2023-03-17 02:50:31,906] [INFO] Task started: fastANI
[2023-03-17 02:50:31,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9b5f6a-bdc0-4876-85c4-eb9328d9342e/OceanDNA-b16552.fa --refList OceanDNA-b16552/target_genomes_gtdb.txt --output OceanDNA-b16552/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:35,053] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:35,058] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:50:35,058] [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_013911515.1	s__Synechococcus_E sp013911515	99.0942	270	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014279895.1	s__Synechococcus_E sp002724845	91.3752	292	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCF_000161795.2	s__Synechococcus_E sp000161795	90.7124	282	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012625.1	s__Synechococcus_E sp000012625	90.4833	290	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCA_016779825.1	s__Synechococcus_E sp016779825	88.9892	239	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737595.1	s__Synechococcus_E sp000737595	87.926	277	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900474185.1	s__Synechococcus_E sp900474185	85.7891	283	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
GCF_014279755.1	s__Synechococcus_E sp014279755	85.7045	281	298	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:35,060] [INFO] GTDB search result was written to OceanDNA-b16552/result_gtdb.tsv
[2023-03-17 02:50:35,061] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:35,063] [INFO] DFAST_QC result json was written to OceanDNA-b16552/dqc_result.json
[2023-03-17 02:50:35,063] [INFO] DFAST_QC completed!
[2023-03-17 02:50:35,064] [INFO] Total running time: 0h0m58s