[2023-06-27 10:38:37,205] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:38:37,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:38:37,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference
[2023-06-27 10:38:40,245] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:38:40,246] [INFO] Task started: Prodigal
[2023-06-27 10:38:40,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5927c1b-59d9-4ac3-88ec-6d227507b3f7/GCA_002310195.1_ASM231019v1_genomic.fna.gz | prodigal -d GCA_002310195.1_ASM231019v1_genomic.fna/cds.fna -a GCA_002310195.1_ASM231019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:38:52,249] [INFO] Task succeeded: Prodigal
[2023-06-27 10:38:52,250] [INFO] Task started: HMMsearch
[2023-06-27 10:38:52,250] [INFO] Running command: hmmsearch --tblout GCA_002310195.1_ASM231019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/reference_markers.hmm GCA_002310195.1_ASM231019v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:38:52,509] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:38:52,512] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5927c1b-59d9-4ac3-88ec-6d227507b3f7/GCA_002310195.1_ASM231019v1_genomic.fna.gz]
[2023-06-27 10:38:52,539] [INFO] Query marker FASTA was written to GCA_002310195.1_ASM231019v1_genomic.fna/markers.fasta
[2023-06-27 10:38:52,539] [INFO] Task started: Blastn
[2023-06-27 10:38:52,539] [INFO] Running command: blastn -query GCA_002310195.1_ASM231019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/reference_markers.fasta -out GCA_002310195.1_ASM231019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:38:53,203] [INFO] Task succeeded: Blastn
[2023-06-27 10:38:53,207] [INFO] Selected 22 target genomes.
[2023-06-27 10:38:53,208] [INFO] Target genome list was writen to GCA_002310195.1_ASM231019v1_genomic.fna/target_genomes.txt
[2023-06-27 10:38:53,216] [INFO] Task started: fastANI
[2023-06-27 10:38:53,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5927c1b-59d9-4ac3-88ec-6d227507b3f7/GCA_002310195.1_ASM231019v1_genomic.fna.gz --refList GCA_002310195.1_ASM231019v1_genomic.fna/target_genomes.txt --output GCA_002310195.1_ASM231019v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:39:08,052] [INFO] Task succeeded: fastANI
[2023-06-27 10:39:08,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:39:08,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:39:08,055] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:39:08,055] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 10:39:08,055] [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 10:39:08,058] [INFO] DFAST Taxonomy check result was written to GCA_002310195.1_ASM231019v1_genomic.fna/tc_result.tsv
[2023-06-27 10:39:08,058] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:39:08,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:39:08,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/checkm_data
[2023-06-27 10:39:08,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:39:08,091] [INFO] Task started: CheckM
[2023-06-27 10:39:08,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310195.1_ASM231019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310195.1_ASM231019v1_genomic.fna/checkm_input GCA_002310195.1_ASM231019v1_genomic.fna/checkm_result
[2023-06-27 10:39:46,143] [INFO] Task succeeded: CheckM
[2023-06-27 10:39:46,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:39:46,165] [INFO] ===== Completeness check finished =====
[2023-06-27 10:39:46,165] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:39:46,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310195.1_ASM231019v1_genomic.fna/markers.fasta)
[2023-06-27 10:39:46,165] [INFO] Task started: Blastn
[2023-06-27 10:39:46,166] [INFO] Running command: blastn -query GCA_002310195.1_ASM231019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02acc932-10c2-41eb-979b-4948c0dd1d05/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310195.1_ASM231019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:39:47,037] [INFO] Task succeeded: Blastn
[2023-06-27 10:39:47,041] [INFO] Selected 10 target genomes.
[2023-06-27 10:39:47,042] [INFO] Target genome list was writen to GCA_002310195.1_ASM231019v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:39:47,047] [INFO] Task started: fastANI
[2023-06-27 10:39:47,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5927c1b-59d9-4ac3-88ec-6d227507b3f7/GCA_002310195.1_ASM231019v1_genomic.fna.gz --refList GCA_002310195.1_ASM231019v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310195.1_ASM231019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:39:52,010] [INFO] Task succeeded: fastANI
[2023-06-27 10:39:52,020] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 10:39:52,020] [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_002310195.1	s__RF16 sp002310195	100.0	640	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.66	96.21	0.77	0.73	4	conclusive
GCA_017525455.1	s__RF16 sp017525455	82.6464	317	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783545.1	s__RF16 sp902783545	80.8619	265	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792835.1	s__RF16 sp902792835	80.7747	256	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.43	96.27	0.83	0.80	3	-
GCA_905233935.1	s__RF16 sp905233935	80.7057	289	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317745.1	s__RF16 sp900317745	80.6814	317	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.61	95.58	0.85	0.81	17	-
GCA_017444065.1	s__RF16 sp017444065	80.5147	359	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798965.1	s__RF16 sp902798965	79.7064	289	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443075.1	s__RF16 sp017443075	79.3925	242	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317885.1	s__RF16 sp900317885	77.3284	91	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.25	96.25	0.86	0.83	5	-
--------------------------------------------------------------------------------
[2023-06-27 10:39:52,022] [INFO] GTDB search result was written to GCA_002310195.1_ASM231019v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:39:52,023] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:39:52,028] [INFO] DFAST_QC result json was written to GCA_002310195.1_ASM231019v1_genomic.fna/dqc_result.json
[2023-06-27 10:39:52,028] [INFO] DFAST_QC completed!
[2023-06-27 10:39:52,028] [INFO] Total running time: 0h1m15s