[2023-06-04 17:34:33,566] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:34:33,570] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:34:33,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference
[2023-06-04 17:34:36,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:34:36,683] [INFO] Task started: Prodigal
[2023-06-04 17:34:36,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e31a063-6fb1-4d1f-852d-8bbf1845017b/GCA_004213165.1_ASM421316v1_genomic.fna.gz | prodigal -d GCA_004213165.1_ASM421316v1_genomic.fna/cds.fna -a GCA_004213165.1_ASM421316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:34:45,057] [INFO] Task succeeded: Prodigal
[2023-06-04 17:34:45,057] [INFO] Task started: HMMsearch
[2023-06-04 17:34:45,057] [INFO] Running command: hmmsearch --tblout GCA_004213165.1_ASM421316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/reference_markers.hmm GCA_004213165.1_ASM421316v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:34:45,280] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:34:45,282] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e31a063-6fb1-4d1f-852d-8bbf1845017b/GCA_004213165.1_ASM421316v1_genomic.fna.gz]
[2023-06-04 17:34:45,300] [INFO] Query marker FASTA was written to GCA_004213165.1_ASM421316v1_genomic.fna/markers.fasta
[2023-06-04 17:34:45,300] [INFO] Task started: Blastn
[2023-06-04 17:34:45,300] [INFO] Running command: blastn -query GCA_004213165.1_ASM421316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/reference_markers.fasta -out GCA_004213165.1_ASM421316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:34:45,858] [INFO] Task succeeded: Blastn
[2023-06-04 17:34:45,863] [INFO] Selected 22 target genomes.
[2023-06-04 17:34:45,863] [INFO] Target genome list was writen to GCA_004213165.1_ASM421316v1_genomic.fna/target_genomes.txt
[2023-06-04 17:34:45,991] [INFO] Task started: fastANI
[2023-06-04 17:34:45,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e31a063-6fb1-4d1f-852d-8bbf1845017b/GCA_004213165.1_ASM421316v1_genomic.fna.gz --refList GCA_004213165.1_ASM421316v1_genomic.fna/target_genomes.txt --output GCA_004213165.1_ASM421316v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:34:59,816] [INFO] Task succeeded: fastANI
[2023-06-04 17:34:59,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:34:59,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:34:59,824] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:34:59,824] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:34:59,824] [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	76.8069	85	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:34:59,827] [INFO] DFAST Taxonomy check result was written to GCA_004213165.1_ASM421316v1_genomic.fna/tc_result.tsv
[2023-06-04 17:34:59,827] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:34:59,827] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:34:59,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/checkm_data
[2023-06-04 17:34:59,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:34:59,851] [INFO] Task started: CheckM
[2023-06-04 17:34:59,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004213165.1_ASM421316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004213165.1_ASM421316v1_genomic.fna/checkm_input GCA_004213165.1_ASM421316v1_genomic.fna/checkm_result
[2023-06-04 17:35:30,298] [INFO] Task succeeded: CheckM
[2023-06-04 17:35:30,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:35:30,317] [INFO] ===== Completeness check finished =====
[2023-06-04 17:35:30,317] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:35:30,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004213165.1_ASM421316v1_genomic.fna/markers.fasta)
[2023-06-04 17:35:30,318] [INFO] Task started: Blastn
[2023-06-04 17:35:30,319] [INFO] Running command: blastn -query GCA_004213165.1_ASM421316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47089644-6f70-496c-8f54-6ce799b5ccb1/dqc_reference/reference_markers_gtdb.fasta -out GCA_004213165.1_ASM421316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:31,080] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:31,085] [INFO] Selected 15 target genomes.
[2023-06-04 17:35:31,085] [INFO] Target genome list was writen to GCA_004213165.1_ASM421316v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:35:31,401] [INFO] Task started: fastANI
[2023-06-04 17:35:31,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e31a063-6fb1-4d1f-852d-8bbf1845017b/GCA_004213165.1_ASM421316v1_genomic.fna.gz --refList GCA_004213165.1_ASM421316v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004213165.1_ASM421316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:35:37,863] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:37,877] [INFO] Found 11 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-04 17:35:37,877] [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	96.7853	448	453	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	inconclusive
GCA_003214855.1	s__Prochlorococcus_C sp003214855	96.048	316	453	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000760295.1	s__Prochlorococcus_C sp000760295	95.7833	438	453	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	99.99	99.99	0.99	0.99	3	inconclusive
GCF_014279875.1	s__Synechococcus_C sp002172935	76.9751	73	453	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_900474295.1	s__Synechococcus_C sp900474295	76.9195	76	453	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_014217855.1	s__Synechococcus_C sp004332415	76.8985	92	453	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_000195975.1	s__Synechococcus_E sp000195975	76.8069	85	453	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_014304815.1	s__Synechococcus_C sp001632165	76.6982	68	453	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.31	96.03	0.90	0.85	7	-
GCA_002691345.1	s__Synechococcus_E sp002691345	76.6082	50	453	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.96	0.96	2	-
GCF_014279775.1	s__Synechococcus_C sp002500205	76.4755	65	453	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	-
GCA_002690325.1	s__Synechococcus_E sp002690325	76.1437	55	453	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	-
--------------------------------------------------------------------------------
[2023-06-04 17:35:37,879] [INFO] GTDB search result was written to GCA_004213165.1_ASM421316v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:35:37,880] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:35:37,883] [INFO] DFAST_QC result json was written to GCA_004213165.1_ASM421316v1_genomic.fna/dqc_result.json
[2023-06-04 17:35:37,883] [INFO] DFAST_QC completed!
[2023-06-04 17:35:37,883] [INFO] Total running time: 0h1m4s