[2023-06-30 19:48:30,822] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:48:30,836] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:48:30,836] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference
[2023-06-30 19:48:37,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:48:37,143] [INFO] Task started: Prodigal
[2023-06-30 19:48:37,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg29ecc168-1d83-4e3d-b0f2-0641779ba28f/GCA_016708235.1_ASM1670823v1_genomic.fna.gz | prodigal -d GCA_016708235.1_ASM1670823v1_genomic.fna/cds.fna -a GCA_016708235.1_ASM1670823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:49:12,591] [INFO] Task succeeded: Prodigal
[2023-06-30 19:49:12,591] [INFO] Task started: HMMsearch
[2023-06-30 19:49:12,591] [INFO] Running command: hmmsearch --tblout GCA_016708235.1_ASM1670823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/reference_markers.hmm GCA_016708235.1_ASM1670823v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:49:12,953] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:49:12,954] [INFO] Found 6/6 markers.
[2023-06-30 19:49:12,994] [INFO] Query marker FASTA was written to GCA_016708235.1_ASM1670823v1_genomic.fna/markers.fasta
[2023-06-30 19:49:12,995] [INFO] Task started: Blastn
[2023-06-30 19:49:12,995] [INFO] Running command: blastn -query GCA_016708235.1_ASM1670823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/reference_markers.fasta -out GCA_016708235.1_ASM1670823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:49:17,225] [INFO] Task succeeded: Blastn
[2023-06-30 19:49:17,230] [INFO] Selected 29 target genomes.
[2023-06-30 19:49:17,230] [INFO] Target genome list was writen to GCA_016708235.1_ASM1670823v1_genomic.fna/target_genomes.txt
[2023-06-30 19:49:17,323] [INFO] Task started: fastANI
[2023-06-30 19:49:17,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg29ecc168-1d83-4e3d-b0f2-0641779ba28f/GCA_016708235.1_ASM1670823v1_genomic.fna.gz --refList GCA_016708235.1_ASM1670823v1_genomic.fna/target_genomes.txt --output GCA_016708235.1_ASM1670823v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:49:37,987] [INFO] Task succeeded: fastANI
[2023-06-30 19:49:37,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:49:37,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:49:37,991] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:49:37,991] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 19:49:37,992] [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
--------------------------------------------------------------------------------
[2023-06-30 19:49:37,994] [INFO] DFAST Taxonomy check result was written to GCA_016708235.1_ASM1670823v1_genomic.fna/tc_result.tsv
[2023-06-30 19:49:37,995] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:49:37,995] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:49:37,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/checkm_data
[2023-06-30 19:49:38,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:49:38,044] [INFO] Task started: CheckM
[2023-06-30 19:49:38,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708235.1_ASM1670823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708235.1_ASM1670823v1_genomic.fna/checkm_input GCA_016708235.1_ASM1670823v1_genomic.fna/checkm_result
[2023-06-30 19:51:17,005] [INFO] Task succeeded: CheckM
[2023-06-30 19:51:17,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:51:17,028] [INFO] ===== Completeness check finished =====
[2023-06-30 19:51:17,028] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:51:17,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708235.1_ASM1670823v1_genomic.fna/markers.fasta)
[2023-06-30 19:51:17,029] [INFO] Task started: Blastn
[2023-06-30 19:51:17,029] [INFO] Running command: blastn -query GCA_016708235.1_ASM1670823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb586e8-f9c0-423d-84b7-2e0009d0753b/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708235.1_ASM1670823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:51:17,808] [INFO] Task succeeded: Blastn
[2023-06-30 19:51:17,814] [INFO] Selected 16 target genomes.
[2023-06-30 19:51:17,814] [INFO] Target genome list was writen to GCA_016708235.1_ASM1670823v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:51:17,825] [INFO] Task started: fastANI
[2023-06-30 19:51:17,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg29ecc168-1d83-4e3d-b0f2-0641779ba28f/GCA_016708235.1_ASM1670823v1_genomic.fna.gz --refList GCA_016708235.1_ASM1670823v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708235.1_ASM1670823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:51:29,721] [INFO] Task succeeded: fastANI
[2023-06-30 19:51:29,738] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:51:29,738] [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_016710015.1	s__PHOS-HE28 sp016710015	99.6457	1310	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.59	99.44	0.96	0.92	12	conclusive
GCA_902826215.1	s__PHOS-HE28 sp902826215	80.2772	661	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482775.1	s__PHOS-HE28 sp002482775	78.8291	495	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717305.1	s__PHOS-HE28 sp016717305	78.8093	401	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.11	99.05	0.96	0.96	3	-
GCA_016788205.1	s__PHOS-HE28 sp016788205	78.6893	427	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721005.1	s__PHOS-HE28 sp016721005	78.6397	388	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360495.1	s__PHOS-HE28 sp002360495	78.4929	427	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	97.35	97.35	0.85	0.85	2	-
GCA_016718655.1	s__PHOS-HE28 sp016718655	78.4146	381	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.66	98.64	0.87	0.86	3	-
GCA_008016945.1	s__PHOS-HE28 sp008016945	78.2169	381	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787995.1	s__PHOS-HE28 sp016787995	78.1405	301	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702645.1	s__PHOS-HE28 sp016702645	78.0938	370	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788295.1	s__PHOS-HE28 sp016788295	78.092	337	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712025.1	s__PHOS-HE28 sp016712025	77.9873	254	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787985.1	s__PHOS-HE28 sp016787985	77.8344	306	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987895.1	s__PHOS-HE28 sp017987895	77.4778	243	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.66	0.85	0.85	2	-
GCA_018267055.1	s__PHOS-HE28 sp018267055	77.3335	269	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:51:29,747] [INFO] GTDB search result was written to GCA_016708235.1_ASM1670823v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:51:29,748] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:51:29,762] [INFO] DFAST_QC result json was written to GCA_016708235.1_ASM1670823v1_genomic.fna/dqc_result.json
[2023-06-30 19:51:29,762] [INFO] DFAST_QC completed!
[2023-06-30 19:51:29,762] [INFO] Total running time: 0h2m59s