[2023-06-27 13:29:17,708] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:29:17,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:29:17,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference
[2023-06-27 13:29:18,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:29:18,954] [INFO] Task started: Prodigal
[2023-06-27 13:29:18,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg28331eeb-65c0-4121-892a-f486d6e0409c/GCA_027622285.1_ASM2762228v1_genomic.fna.gz | prodigal -d GCA_027622285.1_ASM2762228v1_genomic.fna/cds.fna -a GCA_027622285.1_ASM2762228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:29:21,012] [INFO] Task succeeded: Prodigal
[2023-06-27 13:29:21,012] [INFO] Task started: HMMsearch
[2023-06-27 13:29:21,012] [INFO] Running command: hmmsearch --tblout GCA_027622285.1_ASM2762228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/reference_markers.hmm GCA_027622285.1_ASM2762228v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:29:21,199] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:29:21,200] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28331eeb-65c0-4121-892a-f486d6e0409c/GCA_027622285.1_ASM2762228v1_genomic.fna.gz]
[2023-06-27 13:29:21,215] [INFO] Query marker FASTA was written to GCA_027622285.1_ASM2762228v1_genomic.fna/markers.fasta
[2023-06-27 13:29:21,216] [INFO] Task started: Blastn
[2023-06-27 13:29:21,216] [INFO] Running command: blastn -query GCA_027622285.1_ASM2762228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/reference_markers.fasta -out GCA_027622285.1_ASM2762228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:21,811] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:21,817] [INFO] Selected 10 target genomes.
[2023-06-27 13:29:21,818] [INFO] Target genome list was writen to GCA_027622285.1_ASM2762228v1_genomic.fna/target_genomes.txt
[2023-06-27 13:29:21,821] [INFO] Task started: fastANI
[2023-06-27 13:29:21,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg28331eeb-65c0-4121-892a-f486d6e0409c/GCA_027622285.1_ASM2762228v1_genomic.fna.gz --refList GCA_027622285.1_ASM2762228v1_genomic.fna/target_genomes.txt --output GCA_027622285.1_ASM2762228v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:29:25,923] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:25,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:29:25,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:29:25,926] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:29:25,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 13:29:25,926] [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
--------------------------------------------------------------------------------
[2023-06-27 13:29:25,927] [INFO] DFAST Taxonomy check result was written to GCA_027622285.1_ASM2762228v1_genomic.fna/tc_result.tsv
[2023-06-27 13:29:25,928] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:29:25,928] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:29:25,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/checkm_data
[2023-06-27 13:29:25,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:29:25,951] [INFO] Task started: CheckM
[2023-06-27 13:29:25,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027622285.1_ASM2762228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027622285.1_ASM2762228v1_genomic.fna/checkm_input GCA_027622285.1_ASM2762228v1_genomic.fna/checkm_result
[2023-06-27 13:29:41,118] [INFO] Task succeeded: CheckM
[2023-06-27 13:29:41,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 13:29:41,143] [INFO] ===== Completeness check finished =====
[2023-06-27 13:29:41,143] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:29:41,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027622285.1_ASM2762228v1_genomic.fna/markers.fasta)
[2023-06-27 13:29:41,144] [INFO] Task started: Blastn
[2023-06-27 13:29:41,144] [INFO] Running command: blastn -query GCA_027622285.1_ASM2762228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg348740b1-111a-405b-bf0e-7d22b2f224a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_027622285.1_ASM2762228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:42,134] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:42,138] [INFO] Selected 10 target genomes.
[2023-06-27 13:29:42,138] [INFO] Target genome list was writen to GCA_027622285.1_ASM2762228v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:29:42,148] [INFO] Task started: fastANI
[2023-06-27 13:29:42,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg28331eeb-65c0-4121-892a-f486d6e0409c/GCA_027622285.1_ASM2762228v1_genomic.fna.gz --refList GCA_027622285.1_ASM2762228v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027622285.1_ASM2762228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:29:44,577] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:44,587] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:29:44,587] [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
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	95.8831	217	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	conclusive
GCA_902556355.1	s__SCGC-AAA076-P13 sp902556355	82.0384	181	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	81.9608	198	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	81.7412	244	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	81.6495	176	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	81.1141	186	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	80.9645	221	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	80.8889	189	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	79.0572	199	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_002710265.1	s__SAR86A sp002710265	76.7872	71	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:29:44,590] [INFO] GTDB search result was written to GCA_027622285.1_ASM2762228v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:29:44,591] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:29:44,594] [INFO] DFAST_QC result json was written to GCA_027622285.1_ASM2762228v1_genomic.fna/dqc_result.json
[2023-06-27 13:29:44,595] [INFO] DFAST_QC completed!
[2023-06-27 13:29:44,595] [INFO] Total running time: 0h0m27s