[2023-07-01 01:29:16,479] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:29:16,483] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:29:16,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference
[2023-07-01 01:29:18,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:29:18,917] [INFO] Task started: Prodigal
[2023-07-01 01:29:18,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgaca125fd-70d0-4b8f-a974-16ab2620851d/GCA_024276035.1_ASM2427603v1_genomic.fna.gz | prodigal -d GCA_024276035.1_ASM2427603v1_genomic.fna/cds.fna -a GCA_024276035.1_ASM2427603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:29:25,445] [INFO] Task succeeded: Prodigal
[2023-07-01 01:29:25,446] [INFO] Task started: HMMsearch
[2023-07-01 01:29:25,446] [INFO] Running command: hmmsearch --tblout GCA_024276035.1_ASM2427603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/reference_markers.hmm GCA_024276035.1_ASM2427603v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:29:25,684] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:29:25,686] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaca125fd-70d0-4b8f-a974-16ab2620851d/GCA_024276035.1_ASM2427603v1_genomic.fna.gz]
[2023-07-01 01:29:25,722] [INFO] Query marker FASTA was written to GCA_024276035.1_ASM2427603v1_genomic.fna/markers.fasta
[2023-07-01 01:29:25,722] [INFO] Task started: Blastn
[2023-07-01 01:29:25,722] [INFO] Running command: blastn -query GCA_024276035.1_ASM2427603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/reference_markers.fasta -out GCA_024276035.1_ASM2427603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:29:26,395] [INFO] Task succeeded: Blastn
[2023-07-01 01:29:26,400] [INFO] Selected 25 target genomes.
[2023-07-01 01:29:26,400] [INFO] Target genome list was writen to GCA_024276035.1_ASM2427603v1_genomic.fna/target_genomes.txt
[2023-07-01 01:29:26,405] [INFO] Task started: fastANI
[2023-07-01 01:29:26,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca125fd-70d0-4b8f-a974-16ab2620851d/GCA_024276035.1_ASM2427603v1_genomic.fna.gz --refList GCA_024276035.1_ASM2427603v1_genomic.fna/target_genomes.txt --output GCA_024276035.1_ASM2427603v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:29:43,367] [INFO] Task succeeded: fastANI
[2023-07-01 01:29:43,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:29:43,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:29:43,376] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:29:43,376] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:29:43,377] [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
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	75.8943	54	697	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	75.8726	55	697	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:29:43,379] [INFO] DFAST Taxonomy check result was written to GCA_024276035.1_ASM2427603v1_genomic.fna/tc_result.tsv
[2023-07-01 01:29:43,379] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:29:43,380] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:29:43,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/checkm_data
[2023-07-01 01:29:43,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:29:43,415] [INFO] Task started: CheckM
[2023-07-01 01:29:43,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024276035.1_ASM2427603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024276035.1_ASM2427603v1_genomic.fna/checkm_input GCA_024276035.1_ASM2427603v1_genomic.fna/checkm_result
[2023-07-01 01:30:08,817] [INFO] Task succeeded: CheckM
[2023-07-01 01:30:08,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 01:30:08,844] [INFO] ===== Completeness check finished =====
[2023-07-01 01:30:08,844] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:30:08,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024276035.1_ASM2427603v1_genomic.fna/markers.fasta)
[2023-07-01 01:30:08,846] [INFO] Task started: Blastn
[2023-07-01 01:30:08,846] [INFO] Running command: blastn -query GCA_024276035.1_ASM2427603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a77f04-f5f5-418e-a92d-bce35961bebf/dqc_reference/reference_markers_gtdb.fasta -out GCA_024276035.1_ASM2427603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:30:09,916] [INFO] Task succeeded: Blastn
[2023-07-01 01:30:09,921] [INFO] Selected 27 target genomes.
[2023-07-01 01:30:09,921] [INFO] Target genome list was writen to GCA_024276035.1_ASM2427603v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:30:09,929] [INFO] Task started: fastANI
[2023-07-01 01:30:09,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca125fd-70d0-4b8f-a974-16ab2620851d/GCA_024276035.1_ASM2427603v1_genomic.fna.gz --refList GCA_024276035.1_ASM2427603v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024276035.1_ASM2427603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:30:26,397] [INFO] Task succeeded: fastANI
[2023-07-01 01:30:26,416] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 01:30:26,416] [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_003694975.1	s__J097 sp003694975	80.9964	352	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__J097	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152325.1	s__Desulfolinea sp013152325	77.5609	212	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	77.0313	132	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187665.1	s__UBA7227 sp019187665	76.4829	75	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418215.1	s__UBA5796 sp002418215	76.465	163	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5796	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489255.1	s__S143-42 sp015489255	76.4498	61	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__S143-42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112685.1	s__OLB14 sp013112685	76.3911	79	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418205.1	s__UBA12294 sp002418205	76.3783	55	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.83	99.80	0.91	0.90	3	-
GCA_013360875.1	s__UBA12294 sp013360875	76.1682	71	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388685.1	s__UBA12294 sp013388685	76.1643	80	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223135.1	s__UBA12294 sp016223135	76.0818	96	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.98	99.98	0.97	0.97	2	-
GCA_011046615.1	s__DSPQ01 sp011046615	75.9729	56	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__E44-bin32;g__DSPQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875215.1	s__UBA5195 sp903875215	75.8641	72	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.98	99.95	0.99	0.97	6	-
GCA_011322445.1	s__DRMV01 sp011322445	75.7648	54	697	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__DRMV01	95.0	98.57	98.55	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-07-01 01:30:26,421] [INFO] GTDB search result was written to GCA_024276035.1_ASM2427603v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:30:26,421] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:30:26,424] [INFO] DFAST_QC result json was written to GCA_024276035.1_ASM2427603v1_genomic.fna/dqc_result.json
[2023-07-01 01:30:26,425] [INFO] DFAST_QC completed!
[2023-07-01 01:30:26,425] [INFO] Total running time: 0h1m10s