[2023-06-18 11:02:57,999] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:58,004] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:58,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference
[2023-06-18 11:02:59,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:59,327] [INFO] Task started: Prodigal
[2023-06-18 11:02:59,327] [INFO] Running command: gunzip -c /var/lib/cwl/stgd24954c2-05f2-488f-88f3-c91367322c84/GCA_014533905.1_ASM1453390v1_genomic.fna.gz | prodigal -d GCA_014533905.1_ASM1453390v1_genomic.fna/cds.fna -a GCA_014533905.1_ASM1453390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:03:06,445] [INFO] Task succeeded: Prodigal
[2023-06-18 11:03:06,446] [INFO] Task started: HMMsearch
[2023-06-18 11:03:06,446] [INFO] Running command: hmmsearch --tblout GCA_014533905.1_ASM1453390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/reference_markers.hmm GCA_014533905.1_ASM1453390v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:03:06,729] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:03:06,732] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd24954c2-05f2-488f-88f3-c91367322c84/GCA_014533905.1_ASM1453390v1_genomic.fna.gz]
[2023-06-18 11:03:06,774] [INFO] Query marker FASTA was written to GCA_014533905.1_ASM1453390v1_genomic.fna/markers.fasta
[2023-06-18 11:03:06,775] [INFO] Task started: Blastn
[2023-06-18 11:03:06,775] [INFO] Running command: blastn -query GCA_014533905.1_ASM1453390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/reference_markers.fasta -out GCA_014533905.1_ASM1453390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:07,348] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:07,355] [INFO] Selected 16 target genomes.
[2023-06-18 11:03:07,355] [INFO] Target genome list was writen to GCA_014533905.1_ASM1453390v1_genomic.fna/target_genomes.txt
[2023-06-18 11:03:07,358] [INFO] Task started: fastANI
[2023-06-18 11:03:07,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgd24954c2-05f2-488f-88f3-c91367322c84/GCA_014533905.1_ASM1453390v1_genomic.fna.gz --refList GCA_014533905.1_ASM1453390v1_genomic.fna/target_genomes.txt --output GCA_014533905.1_ASM1453390v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:03:23,090] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:23,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:03:23,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:03:23,094] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:03:23,094] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:03:23,094] [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
--------------------------------------------------------------------------------
[2023-06-18 11:03:23,099] [INFO] DFAST Taxonomy check result was written to GCA_014533905.1_ASM1453390v1_genomic.fna/tc_result.tsv
[2023-06-18 11:03:23,100] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:03:23,101] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:03:23,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/checkm_data
[2023-06-18 11:03:23,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:03:23,150] [INFO] Task started: CheckM
[2023-06-18 11:03:23,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014533905.1_ASM1453390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014533905.1_ASM1453390v1_genomic.fna/checkm_input GCA_014533905.1_ASM1453390v1_genomic.fna/checkm_result
[2023-06-18 11:03:50,487] [INFO] Task succeeded: CheckM
[2023-06-18 11:03:50,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.13%
Contamintation: 14.43%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-18 11:03:50,528] [INFO] ===== Completeness check finished =====
[2023-06-18 11:03:50,528] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:03:50,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014533905.1_ASM1453390v1_genomic.fna/markers.fasta)
[2023-06-18 11:03:50,529] [INFO] Task started: Blastn
[2023-06-18 11:03:50,529] [INFO] Running command: blastn -query GCA_014533905.1_ASM1453390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2529370c-ce73-4e17-8e64-24a85bd42915/dqc_reference/reference_markers_gtdb.fasta -out GCA_014533905.1_ASM1453390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:51,329] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:51,337] [INFO] Selected 21 target genomes.
[2023-06-18 11:03:51,337] [INFO] Target genome list was writen to GCA_014533905.1_ASM1453390v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:03:51,384] [INFO] Task started: fastANI
[2023-06-18 11:03:51,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgd24954c2-05f2-488f-88f3-c91367322c84/GCA_014533905.1_ASM1453390v1_genomic.fna.gz --refList GCA_014533905.1_ASM1453390v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014533905.1_ASM1453390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:04:14,635] [INFO] Task succeeded: fastANI
[2023-06-18 11:04:14,646] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 11:04:14,646] [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_014695295.1	s__Microcoleus sp014695295	94.5913	141	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013179805.1	s__Microcoleus asticus	94.1465	142	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214075.1	s__Microcoleus vaginatus	93.7094	138	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317475.1	s__Microcoleus sp000317475	93.5322	141	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695175.1	s__Microcoleus sp014695175	93.0707	139	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	96.46	96.46	0.87	0.87	3	-
GCA_004293365.1	s__Microcoleus sp004293365	89.1699	137	148	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.86	99.75	0.98	0.97	5	-
--------------------------------------------------------------------------------
[2023-06-18 11:04:14,648] [INFO] GTDB search result was written to GCA_014533905.1_ASM1453390v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:04:14,649] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:04:14,653] [INFO] DFAST_QC result json was written to GCA_014533905.1_ASM1453390v1_genomic.fna/dqc_result.json
[2023-06-18 11:04:14,653] [INFO] DFAST_QC completed!
[2023-06-18 11:04:14,653] [INFO] Total running time: 0h1m17s