[2023-06-30 00:24:27,014] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:24:27,016] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:24:27,016] [INFO] DQC Reference Directory: /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference
[2023-06-30 00:24:28,253] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:24:28,254] [INFO] Task started: Prodigal
[2023-06-30 00:24:28,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dddb142-0c91-40d8-882a-91bfbbda6e9a/GCA_024228965.1_ASM2422896v1_genomic.fna.gz | prodigal -d GCA_024228965.1_ASM2422896v1_genomic.fna/cds.fna -a GCA_024228965.1_ASM2422896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:24:39,054] [INFO] Task succeeded: Prodigal
[2023-06-30 00:24:39,054] [INFO] Task started: HMMsearch
[2023-06-30 00:24:39,055] [INFO] Running command: hmmsearch --tblout GCA_024228965.1_ASM2422896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/reference_markers.hmm GCA_024228965.1_ASM2422896v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:24:39,285] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:24:39,286] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6dddb142-0c91-40d8-882a-91bfbbda6e9a/GCA_024228965.1_ASM2422896v1_genomic.fna.gz]
[2023-06-30 00:24:39,317] [INFO] Query marker FASTA was written to GCA_024228965.1_ASM2422896v1_genomic.fna/markers.fasta
[2023-06-30 00:24:39,317] [INFO] Task started: Blastn
[2023-06-30 00:24:39,317] [INFO] Running command: blastn -query GCA_024228965.1_ASM2422896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/reference_markers.fasta -out GCA_024228965.1_ASM2422896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:24:39,901] [INFO] Task succeeded: Blastn
[2023-06-30 00:24:39,906] [INFO] Selected 22 target genomes.
[2023-06-30 00:24:39,906] [INFO] Target genome list was writen to GCA_024228965.1_ASM2422896v1_genomic.fna/target_genomes.txt
[2023-06-30 00:24:39,910] [INFO] Task started: fastANI
[2023-06-30 00:24:39,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dddb142-0c91-40d8-882a-91bfbbda6e9a/GCA_024228965.1_ASM2422896v1_genomic.fna.gz --refList GCA_024228965.1_ASM2422896v1_genomic.fna/target_genomes.txt --output GCA_024228965.1_ASM2422896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:24:54,356] [INFO] Task succeeded: fastANI
[2023-06-30 00:24:54,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:24:54,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:24:54,362] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:24:54,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:24:54,363] [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	77.1228	52	318	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:24:54,365] [INFO] DFAST Taxonomy check result was written to GCA_024228965.1_ASM2422896v1_genomic.fna/tc_result.tsv
[2023-06-30 00:24:54,365] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:24:54,366] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:24:54,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/checkm_data
[2023-06-30 00:24:54,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:24:54,397] [INFO] Task started: CheckM
[2023-06-30 00:24:54,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024228965.1_ASM2422896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024228965.1_ASM2422896v1_genomic.fna/checkm_input GCA_024228965.1_ASM2422896v1_genomic.fna/checkm_result
[2023-06-30 00:25:22,351] [INFO] Task succeeded: CheckM
[2023-06-30 00:25:22,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.88%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-30 00:25:22,376] [INFO] ===== Completeness check finished =====
[2023-06-30 00:25:22,377] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:25:22,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024228965.1_ASM2422896v1_genomic.fna/markers.fasta)
[2023-06-30 00:25:22,377] [INFO] Task started: Blastn
[2023-06-30 00:25:22,378] [INFO] Running command: blastn -query GCA_024228965.1_ASM2422896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd121f6cc-68dc-4b82-8243-3545b72a4b04/dqc_reference/reference_markers_gtdb.fasta -out GCA_024228965.1_ASM2422896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:25:23,147] [INFO] Task succeeded: Blastn
[2023-06-30 00:25:23,152] [INFO] Selected 28 target genomes.
[2023-06-30 00:25:23,152] [INFO] Target genome list was writen to GCA_024228965.1_ASM2422896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:25:23,195] [INFO] Task started: fastANI
[2023-06-30 00:25:23,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dddb142-0c91-40d8-882a-91bfbbda6e9a/GCA_024228965.1_ASM2422896v1_genomic.fna.gz --refList GCA_024228965.1_ASM2422896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024228965.1_ASM2422896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:25:33,879] [INFO] Task succeeded: fastANI
[2023-06-30 00:25:33,900] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:25:33,900] [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_000011485.1	s__Prochlorococcus_C marinus_B	78.1728	117	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	96.34	95.12	0.90	0.85	19	-
GCF_014279895.1	s__Synechococcus_E sp002724845	77.8016	54	318	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_014217855.1	s__Synechococcus_C sp004332415	77.6044	65	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.38	96.99	0.88	0.86	3	-
GCF_000161795.2	s__Synechococcus_E sp000161795	77.5531	53	318	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_014279755.1	s__Synechococcus_E sp014279755	77.466	56	318	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_000153825.1	s__Synechococcus_C sp000153825	77.4005	61	318	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_014279595.1	s__Synechococcus_C sp000153065	77.207	57	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
GCF_900473935.1	s__Synechococcus_C sp002171995	77.1631	62	318	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	-
GCF_900474295.1	s__Synechococcus_C sp900474295	77.1618	65	318	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	77.1228	52	318	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_004209775.1	s__Synechococcus_C sp004209775	77.116	64	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900474185.1	s__Synechococcus_E sp900474185	77.0856	55	318	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_014279975.1	s__Synechococcus_C sp014279975	77.0744	52	318	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_013911515.1	s__Synechococcus_E sp013911515	77.0219	59	318	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_014279875.1	s__Synechococcus_C sp002172935	76.9235	58	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.09	98.09	0.93	0.93	2	-
GCF_014280035.1	s__Synechococcus_C sp002693285	76.7572	63	318	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.86	0.95	0.94	3	-
GCF_014279795.1	s__Synechococcus_C sp014279795	76.5406	60	318	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	-
--------------------------------------------------------------------------------
[2023-06-30 00:25:33,902] [INFO] GTDB search result was written to GCA_024228965.1_ASM2422896v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:25:33,903] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:25:33,906] [INFO] DFAST_QC result json was written to GCA_024228965.1_ASM2422896v1_genomic.fna/dqc_result.json
[2023-06-30 00:25:33,906] [INFO] DFAST_QC completed!
[2023-06-30 00:25:33,906] [INFO] Total running time: 0h1m7s