[2023-06-19 01:46:27,429] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:46:27,432] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:46:27,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference
[2023-06-19 01:46:29,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:46:29,805] [INFO] Task started: Prodigal
[2023-06-19 01:46:29,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd96cd44-6ec3-4b2b-b140-b8899cc314ac/GCA_018652665.1_ASM1865266v1_genomic.fna.gz | prodigal -d GCA_018652665.1_ASM1865266v1_genomic.fna/cds.fna -a GCA_018652665.1_ASM1865266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:46:31,159] [INFO] Task succeeded: Prodigal
[2023-06-19 01:46:31,159] [INFO] Task started: HMMsearch
[2023-06-19 01:46:31,159] [INFO] Running command: hmmsearch --tblout GCA_018652665.1_ASM1865266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/reference_markers.hmm GCA_018652665.1_ASM1865266v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:46:31,452] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:46:31,454] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd96cd44-6ec3-4b2b-b140-b8899cc314ac/GCA_018652665.1_ASM1865266v1_genomic.fna.gz]
[2023-06-19 01:46:31,471] [INFO] Query marker FASTA was written to GCA_018652665.1_ASM1865266v1_genomic.fna/markers.fasta
[2023-06-19 01:46:31,474] [INFO] Task started: Blastn
[2023-06-19 01:46:31,474] [INFO] Running command: blastn -query GCA_018652665.1_ASM1865266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/reference_markers.fasta -out GCA_018652665.1_ASM1865266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:34,433] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:34,438] [INFO] Selected 15 target genomes.
[2023-06-19 01:46:34,438] [INFO] Target genome list was writen to GCA_018652665.1_ASM1865266v1_genomic.fna/target_genomes.txt
[2023-06-19 01:46:34,463] [INFO] Task started: fastANI
[2023-06-19 01:46:34,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd96cd44-6ec3-4b2b-b140-b8899cc314ac/GCA_018652665.1_ASM1865266v1_genomic.fna.gz --refList GCA_018652665.1_ASM1865266v1_genomic.fna/target_genomes.txt --output GCA_018652665.1_ASM1865266v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:46:42,003] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:42,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:46:42,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:46:42,006] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:46:42,006] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 01:46:42,006] [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
--------------------------------------------------------------------------------
[2023-06-19 01:46:42,008] [INFO] DFAST Taxonomy check result was written to GCA_018652665.1_ASM1865266v1_genomic.fna/tc_result.tsv
[2023-06-19 01:46:42,009] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:46:42,009] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:46:42,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/checkm_data
[2023-06-19 01:46:42,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:46:42,027] [INFO] Task started: CheckM
[2023-06-19 01:46:42,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018652665.1_ASM1865266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018652665.1_ASM1865266v1_genomic.fna/checkm_input GCA_018652665.1_ASM1865266v1_genomic.fna/checkm_result
[2023-06-19 01:46:54,936] [INFO] Task succeeded: CheckM
[2023-06-19 01:46:54,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:46:54,964] [INFO] ===== Completeness check finished =====
[2023-06-19 01:46:54,965] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:46:54,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018652665.1_ASM1865266v1_genomic.fna/markers.fasta)
[2023-06-19 01:46:54,966] [INFO] Task started: Blastn
[2023-06-19 01:46:54,966] [INFO] Running command: blastn -query GCA_018652665.1_ASM1865266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e68ffe6-5b27-482b-9b18-16ec4f659e4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018652665.1_ASM1865266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:55,410] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:55,415] [INFO] Selected 8 target genomes.
[2023-06-19 01:46:55,415] [INFO] Target genome list was writen to GCA_018652665.1_ASM1865266v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:46:55,416] [INFO] Task started: fastANI
[2023-06-19 01:46:55,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd96cd44-6ec3-4b2b-b140-b8899cc314ac/GCA_018652665.1_ASM1865266v1_genomic.fna.gz --refList GCA_018652665.1_ASM1865266v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018652665.1_ASM1865266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:46:57,018] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:57,038] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:46:57,040] [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_000402755.1	s__Marinisoma sp000402755	95.63	211	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	conclusive
GCA_905182795.1	s__Marinisoma sp905182795	90.032	232	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701645.1	s__Marinisoma sp002701645	86.3943	173	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	86.2423	202	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_000402815.1	s__Marinisoma atlanticum	83.5809	227	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902624275.1	s__Marinisoma sp902624275	77.317	76	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578385.1	s__Marinisoma sp002710515	77.2526	90	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_000402655.1	s__Marinisoma sp000402655	77.1872	77	257	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-19 01:46:57,044] [INFO] GTDB search result was written to GCA_018652665.1_ASM1865266v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:46:57,045] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:46:57,055] [INFO] DFAST_QC result json was written to GCA_018652665.1_ASM1865266v1_genomic.fna/dqc_result.json
[2023-06-19 01:46:57,057] [INFO] DFAST_QC completed!
[2023-06-19 01:46:57,057] [INFO] Total running time: 0h0m30s