[2023-06-04 18:00:17,691] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:17,693] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:17,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference
[2023-06-04 18:00:18,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:18,956] [INFO] Task started: Prodigal
[2023-06-04 18:00:18,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg36d64d21-f291-4959-9b92-37d44c87bca1/GCA_902522905.1_AG-895-D03_genomic.fna.gz | prodigal -d GCA_902522905.1_AG-895-D03_genomic.fna/cds.fna -a GCA_902522905.1_AG-895-D03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:22,189] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:22,190] [INFO] Task started: HMMsearch
[2023-06-04 18:00:22,190] [INFO] Running command: hmmsearch --tblout GCA_902522905.1_AG-895-D03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/reference_markers.hmm GCA_902522905.1_AG-895-D03_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:22,413] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:22,414] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg36d64d21-f291-4959-9b92-37d44c87bca1/GCA_902522905.1_AG-895-D03_genomic.fna.gz]
[2023-06-04 18:00:22,443] [INFO] Query marker FASTA was written to GCA_902522905.1_AG-895-D03_genomic.fna/markers.fasta
[2023-06-04 18:00:22,444] [INFO] Task started: Blastn
[2023-06-04 18:00:22,444] [INFO] Running command: blastn -query GCA_902522905.1_AG-895-D03_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/reference_markers.fasta -out GCA_902522905.1_AG-895-D03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:23,006] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:23,010] [INFO] Selected 14 target genomes.
[2023-06-04 18:00:23,010] [INFO] Target genome list was writen to GCA_902522905.1_AG-895-D03_genomic.fna/target_genomes.txt
[2023-06-04 18:00:23,097] [INFO] Task started: fastANI
[2023-06-04 18:00:23,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg36d64d21-f291-4959-9b92-37d44c87bca1/GCA_902522905.1_AG-895-D03_genomic.fna.gz --refList GCA_902522905.1_AG-895-D03_genomic.fna/target_genomes.txt --output GCA_902522905.1_AG-895-D03_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:29,780] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:29,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:29,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:29,783] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:29,783] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:00:29,783] [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
--------------------------------------------------------------------------------
[2023-06-04 18:00:29,825] [INFO] DFAST Taxonomy check result was written to GCA_902522905.1_AG-895-D03_genomic.fna/tc_result.tsv
[2023-06-04 18:00:29,826] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:29,826] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:29,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/checkm_data
[2023-06-04 18:00:29,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:29,846] [INFO] Task started: CheckM
[2023-06-04 18:00:29,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902522905.1_AG-895-D03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902522905.1_AG-895-D03_genomic.fna/checkm_input GCA_902522905.1_AG-895-D03_genomic.fna/checkm_result
[2023-06-04 18:00:47,295] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:47,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:47,321] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:47,322] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:47,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902522905.1_AG-895-D03_genomic.fna/markers.fasta)
[2023-06-04 18:00:47,323] [INFO] Task started: Blastn
[2023-06-04 18:00:47,323] [INFO] Running command: blastn -query GCA_902522905.1_AG-895-D03_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e1e1d6-04cc-4991-badc-9f7a78ee15e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902522905.1_AG-895-D03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:48,143] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:48,155] [INFO] Selected 24 target genomes.
[2023-06-04 18:00:48,155] [INFO] Target genome list was writen to GCA_902522905.1_AG-895-D03_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:48,612] [INFO] Task started: fastANI
[2023-06-04 18:00:48,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg36d64d21-f291-4959-9b92-37d44c87bca1/GCA_902522905.1_AG-895-D03_genomic.fna.gz --refList GCA_902522905.1_AG-895-D03_genomic.fna/target_genomes_gtdb.txt --output GCA_902522905.1_AG-895-D03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:00:54,880] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:54,914] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:00:54,914] [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_001989455.1	s__Prochlorococcus_A sp001989455	96.0773	310	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.32	95.99	0.94	0.88	36	conclusive
GCA_000635495.1	s__Prochlorococcus_A sp000635495	94.9428	286	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	98.33	95.15	0.88	0.77	73	-
GCA_902611225.1	s__Prochlorococcus_A sp902611225	94.6829	189	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.12	95.12	0.67	0.67	2	-
GCA_003278855.1	s__Prochlorococcus_A sp003278855	94.6756	256	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000634215.1	s__Prochlorococcus_A sp000634215	94.6283	274	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	98.63	98.32	0.87	0.81	20	-
GCF_001180245.1	s__Prochlorococcus_A marinus_F	94.4901	264	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001180325.1	s__Prochlorococcus_A marinus_R	94.3253	249	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278845.1	s__Prochlorococcus_A sp003278845	94.2188	242	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.97	96.38	0.80	0.73	6	-
GCA_003213375.1	s__Prochlorococcus_A sp003213375	94.0354	180	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.27	96.27	0.94	0.94	2	-
GCA_003278765.1	s__Prochlorococcus_A sp003278765	93.9494	240	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216915.1	s__Prochlorococcus_A sp003216915	93.7885	254	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278045.1	s__Prochlorococcus_A sp003278045	93.7391	239	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591275.1	s__Prochlorococcus_A sp902591275	93.7173	180	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536775.1	s__Prochlorococcus_A sp902536775	93.6509	197	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213855.1	s__Prochlorococcus_A sp003213855	93.5825	218	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537275.1	s__Prochlorococcus_A sp902537275	93.4638	158	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537445.1	s__Prochlorococcus_A sp902537445	93.3893	186	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211955.1	s__Prochlorococcus_A sp003211955	93.3877	198	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558895.1	s__Prochlorococcus_A sp902558895	93.3675	205	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281635.1	s__Prochlorococcus_A sp003281635	93.3332	216	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211415.1	s__Prochlorococcus_A sp003211415	92.5748	193	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.46	95.46	0.66	0.66	2	-
GCA_003214215.1	s__Prochlorococcus_A sp003214215	92.2239	178	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216535.1	s__Prochlorococcus_A sp003216535	92.1437	276	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759855.1	s__Prochlorococcus_A marinus_N	88.3063	287	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	99.96	99.95	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-04 18:00:54,917] [INFO] GTDB search result was written to GCA_902522905.1_AG-895-D03_genomic.fna/result_gtdb.tsv
[2023-06-04 18:00:54,917] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:00:54,922] [INFO] DFAST_QC result json was written to GCA_902522905.1_AG-895-D03_genomic.fna/dqc_result.json
[2023-06-04 18:00:54,923] [INFO] DFAST_QC completed!
[2023-06-04 18:00:54,923] [INFO] Total running time: 0h0m37s