[2023-06-17 05:27:05,242] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:27:05,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:27:05,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference
[2023-06-17 05:27:07,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:27:07,319] [INFO] Task started: Prodigal
[2023-06-17 05:27:07,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgcee4d26f-59d8-461b-90a8-dc05e45b8c62/GCA_003449415.1_ASM344941v1_genomic.fna.gz | prodigal -d GCA_003449415.1_ASM344941v1_genomic.fna/cds.fna -a GCA_003449415.1_ASM344941v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:27:09,809] [INFO] Task succeeded: Prodigal
[2023-06-17 05:27:09,810] [INFO] Task started: HMMsearch
[2023-06-17 05:27:09,810] [INFO] Running command: hmmsearch --tblout GCA_003449415.1_ASM344941v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/reference_markers.hmm GCA_003449415.1_ASM344941v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:27:10,060] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:27:10,061] [INFO] Found 6/6 markers.
[2023-06-17 05:27:10,078] [INFO] Query marker FASTA was written to GCA_003449415.1_ASM344941v1_genomic.fna/markers.fasta
[2023-06-17 05:27:10,078] [INFO] Task started: Blastn
[2023-06-17 05:27:10,079] [INFO] Running command: blastn -query GCA_003449415.1_ASM344941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/reference_markers.fasta -out GCA_003449415.1_ASM344941v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:27:11,487] [INFO] Task succeeded: Blastn
[2023-06-17 05:27:11,492] [INFO] Selected 12 target genomes.
[2023-06-17 05:27:11,492] [INFO] Target genome list was writen to GCA_003449415.1_ASM344941v1_genomic.fna/target_genomes.txt
[2023-06-17 05:27:11,498] [INFO] Task started: fastANI
[2023-06-17 05:27:11,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee4d26f-59d8-461b-90a8-dc05e45b8c62/GCA_003449415.1_ASM344941v1_genomic.fna.gz --refList GCA_003449415.1_ASM344941v1_genomic.fna/target_genomes.txt --output GCA_003449415.1_ASM344941v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:27:15,889] [INFO] Task succeeded: fastANI
[2023-06-17 05:27:15,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:27:15,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:27:15,892] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:27:15,892] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 05:27:15,892] [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
--------------------------------------------------------------------------------
[2023-06-17 05:27:15,894] [INFO] DFAST Taxonomy check result was written to GCA_003449415.1_ASM344941v1_genomic.fna/tc_result.tsv
[2023-06-17 05:27:15,895] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:27:15,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:27:15,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/checkm_data
[2023-06-17 05:27:15,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:27:15,909] [INFO] Task started: CheckM
[2023-06-17 05:27:15,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003449415.1_ASM344941v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003449415.1_ASM344941v1_genomic.fna/checkm_input GCA_003449415.1_ASM344941v1_genomic.fna/checkm_result
[2023-06-17 05:27:30,717] [INFO] Task succeeded: CheckM
[2023-06-17 05:27:30,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:27:30,742] [INFO] ===== Completeness check finished =====
[2023-06-17 05:27:30,743] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:27:30,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003449415.1_ASM344941v1_genomic.fna/markers.fasta)
[2023-06-17 05:27:30,743] [INFO] Task started: Blastn
[2023-06-17 05:27:30,743] [INFO] Running command: blastn -query GCA_003449415.1_ASM344941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88071ec6-c2b4-4f4c-92ab-afb66d632374/dqc_reference/reference_markers_gtdb.fasta -out GCA_003449415.1_ASM344941v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:27:31,553] [INFO] Task succeeded: Blastn
[2023-06-17 05:27:31,558] [INFO] Selected 7 target genomes.
[2023-06-17 05:27:31,558] [INFO] Target genome list was writen to GCA_003449415.1_ASM344941v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:27:31,565] [INFO] Task started: fastANI
[2023-06-17 05:27:31,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee4d26f-59d8-461b-90a8-dc05e45b8c62/GCA_003449415.1_ASM344941v1_genomic.fna.gz --refList GCA_003449415.1_ASM344941v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003449415.1_ASM344941v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:27:32,987] [INFO] Task succeeded: fastANI
[2023-06-17 05:27:33,004] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:27:33,005] [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_000996895.1	s__UBA8498 sp000996895	99.889	194	201	d__Bacteria;p__Patescibacteria;c__WWE3;o__UBA101185;f__UBA10185;g__UBA8498	95.0	99.86	99.69	0.96	0.93	14	conclusive
GCA_001773135.1	s__UBA8498 sp001773135	82.3661	154	201	d__Bacteria;p__Patescibacteria;c__WWE3;o__UBA101185;f__UBA10185;g__UBA8498	95.0	99.88	99.86	0.95	0.94	4	-
GCA_001773255.1	s__UBA8498 sp001773255	81.5602	133	201	d__Bacteria;p__Patescibacteria;c__WWE3;o__UBA101185;f__UBA10185;g__UBA8498	95.0	99.69	99.65	0.91	0.89	7	-
GCA_001773385.1	s__UBA8498 sp001773385	81.1797	143	201	d__Bacteria;p__Patescibacteria;c__WWE3;o__UBA101185;f__UBA10185;g__UBA8498	95.0	99.86	99.86	0.89	0.89	2	-
GCA_000503835.1	s__UBA8498 sp000503835	80.1886	132	201	d__Bacteria;p__Patescibacteria;c__WWE3;o__UBA101185;f__UBA10185;g__UBA8498	95.0	99.97	99.92	0.99	0.96	18	-
--------------------------------------------------------------------------------
[2023-06-17 05:27:33,007] [INFO] GTDB search result was written to GCA_003449415.1_ASM344941v1_genomic.fna/result_gtdb.tsv
[2023-06-17 05:27:33,009] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:27:33,013] [INFO] DFAST_QC result json was written to GCA_003449415.1_ASM344941v1_genomic.fna/dqc_result.json
[2023-06-17 05:27:33,013] [INFO] DFAST_QC completed!
[2023-06-17 05:27:33,013] [INFO] Total running time: 0h0m28s