[2023-03-16 10:09:24,142] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:09:24,143] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:09:24,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference
[2023-03-16 10:09:25,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:09:25,217] [INFO] Task started: Prodigal
[2023-03-16 10:09:25,217] [INFO] Running command: cat /var/lib/cwl/stg6bcb7450-9cc2-4608-87d7-9295b74da2c8/OceanDNA-b16668.fa | prodigal -d OceanDNA-b16668/cds.fna -a OceanDNA-b16668/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:09:39,646] [INFO] Task succeeded: Prodigal
[2023-03-16 10:09:39,647] [INFO] Task started: HMMsearch
[2023-03-16 10:09:39,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b16668/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/reference_markers.hmm OceanDNA-b16668/protein.faa > /dev/null
[2023-03-16 10:09:39,784] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:09:39,784] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6bcb7450-9cc2-4608-87d7-9295b74da2c8/OceanDNA-b16668.fa]
[2023-03-16 10:09:39,798] [INFO] Query marker FASTA was written to OceanDNA-b16668/markers.fasta
[2023-03-16 10:09:39,799] [INFO] Task started: Blastn
[2023-03-16 10:09:39,799] [INFO] Running command: blastn -query OceanDNA-b16668/markers.fasta -db /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/reference_markers.fasta -out OceanDNA-b16668/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:40,296] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:40,297] [INFO] Selected 13 target genomes.
[2023-03-16 10:09:40,297] [INFO] Target genome list was writen to OceanDNA-b16668/target_genomes.txt
[2023-03-16 10:09:40,330] [INFO] Task started: fastANI
[2023-03-16 10:09:40,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bcb7450-9cc2-4608-87d7-9295b74da2c8/OceanDNA-b16668.fa --refList OceanDNA-b16668/target_genomes.txt --output OceanDNA-b16668/fastani_result.tsv --threads 1
[2023-03-16 10:09:50,174] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:50,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:09:50,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:09:50,178] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:09:50,178] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:09:50,178] [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	77.567	125	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:09:50,178] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16668/tc_result.tsv
[2023-03-16 10:09:50,178] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:09:50,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:09:50,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/checkm_data
[2023-03-16 10:09:50,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:09:50,189] [INFO] Task started: CheckM
[2023-03-16 10:09:50,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16668/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16668/checkm_input OceanDNA-b16668/checkm_result
[2023-03-16 10:10:31,595] [INFO] Task succeeded: CheckM
[2023-03-16 10:10:31,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.31%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:10:31,597] [INFO] ===== Completeness check finished =====
[2023-03-16 10:10:31,597] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:10:31,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16668/markers.fasta)
[2023-03-16 10:10:31,599] [INFO] Task started: Blastn
[2023-03-16 10:10:31,599] [INFO] Running command: blastn -query OceanDNA-b16668/markers.fasta -db /var/lib/cwl/stg44dd7928-3007-46ae-9139-c96220f3abc6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16668/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:10:32,262] [INFO] Task succeeded: Blastn
[2023-03-16 10:10:32,263] [INFO] Selected 14 target genomes.
[2023-03-16 10:10:32,263] [INFO] Target genome list was writen to OceanDNA-b16668/target_genomes_gtdb.txt
[2023-03-16 10:10:32,287] [INFO] Task started: fastANI
[2023-03-16 10:10:32,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bcb7450-9cc2-4608-87d7-9295b74da2c8/OceanDNA-b16668.fa --refList OceanDNA-b16668/target_genomes_gtdb.txt --output OceanDNA-b16668/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:10:39,020] [INFO] Task succeeded: fastANI
[2023-03-16 10:10:39,028] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:10:39,028] [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
GCF_900473935.1	s__Synechococcus_C sp002171995	98.9618	472	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.80	0.86	0.67	4	conclusive
GCF_900474295.1	s__Synechococcus_C sp900474295	94.9264	470	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153825.1	s__Synechococcus_C sp000153825	79.2259	270	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623675.1	s__Synechococcus_C sp018623675	78.3262	129	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523155.1	s__Synechococcus_C sp011523155	77.7353	105	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195975.1	s__Synechococcus_E sp000195975	77.567	125	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCF_000012625.1	s__Synechococcus_E sp000012625	77.4176	129	478	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	-
GCF_014279815.1	s__Synechococcus_C sp014279815	77.278	150	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280195.1	s__Synechococcus_E sp014280195	77.2286	131	478	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_014279795.1	s__Synechococcus_C sp014279795	77.0348	145	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.67	96.56	0.92	0.91	3	-
GCA_000063505.1	s__Synechococcus_C sp000063505	77.021	148	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.52	97.52	0.89	0.89	2	-
GCF_014280175.1	s__Synechococcus_E sp004212765	76.9671	144	478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2023-03-16 10:10:39,028] [INFO] GTDB search result was written to OceanDNA-b16668/result_gtdb.tsv
[2023-03-16 10:10:39,028] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:10:39,029] [INFO] DFAST_QC result json was written to OceanDNA-b16668/dqc_result.json
[2023-03-16 10:10:39,029] [INFO] DFAST_QC completed!
[2023-03-16 10:10:39,029] [INFO] Total running time: 0h1m15s