[2023-06-13 16:47:22,855] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:47:22,864] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:47:22,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference
[2023-06-13 16:47:24,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:47:24,253] [INFO] Task started: Prodigal
[2023-06-13 16:47:24,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgfae077ce-5b81-4bce-aba4-16f165592348/GCA_022708475.1_ASM2270847v1_genomic.fna.gz | prodigal -d GCA_022708475.1_ASM2270847v1_genomic.fna/cds.fna -a GCA_022708475.1_ASM2270847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:47:34,292] [INFO] Task succeeded: Prodigal
[2023-06-13 16:47:34,293] [INFO] Task started: HMMsearch
[2023-06-13 16:47:34,293] [INFO] Running command: hmmsearch --tblout GCA_022708475.1_ASM2270847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/reference_markers.hmm GCA_022708475.1_ASM2270847v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:47:34,543] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:47:34,545] [INFO] Found 6/6 markers.
[2023-06-13 16:47:34,570] [INFO] Query marker FASTA was written to GCA_022708475.1_ASM2270847v1_genomic.fna/markers.fasta
[2023-06-13 16:47:34,570] [INFO] Task started: Blastn
[2023-06-13 16:47:34,570] [INFO] Running command: blastn -query GCA_022708475.1_ASM2270847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/reference_markers.fasta -out GCA_022708475.1_ASM2270847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:47:35,181] [INFO] Task succeeded: Blastn
[2023-06-13 16:47:35,185] [INFO] Selected 29 target genomes.
[2023-06-13 16:47:35,185] [INFO] Target genome list was writen to GCA_022708475.1_ASM2270847v1_genomic.fna/target_genomes.txt
[2023-06-13 16:47:35,226] [INFO] Task started: fastANI
[2023-06-13 16:47:35,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae077ce-5b81-4bce-aba4-16f165592348/GCA_022708475.1_ASM2270847v1_genomic.fna.gz --refList GCA_022708475.1_ASM2270847v1_genomic.fna/target_genomes.txt --output GCA_022708475.1_ASM2270847v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:47:51,344] [INFO] Task succeeded: fastANI
[2023-06-13 16:47:51,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:47:51,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:47:51,347] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:47:51,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 16:47:51,347] [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
--------------------------------------------------------------------------------
[2023-06-13 16:47:51,349] [INFO] DFAST Taxonomy check result was written to GCA_022708475.1_ASM2270847v1_genomic.fna/tc_result.tsv
[2023-06-13 16:47:51,350] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:47:51,350] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:47:51,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/checkm_data
[2023-06-13 16:47:51,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:47:51,384] [INFO] Task started: CheckM
[2023-06-13 16:47:51,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708475.1_ASM2270847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708475.1_ASM2270847v1_genomic.fna/checkm_input GCA_022708475.1_ASM2270847v1_genomic.fna/checkm_result
[2023-06-13 16:48:25,673] [INFO] Task succeeded: CheckM
[2023-06-13 16:48:25,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:48:25,692] [INFO] ===== Completeness check finished =====
[2023-06-13 16:48:25,693] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:48:25,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708475.1_ASM2270847v1_genomic.fna/markers.fasta)
[2023-06-13 16:48:25,694] [INFO] Task started: Blastn
[2023-06-13 16:48:25,694] [INFO] Running command: blastn -query GCA_022708475.1_ASM2270847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63189397-bea4-430e-a085-a6b8ff9c4b04/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708475.1_ASM2270847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:48:26,519] [INFO] Task succeeded: Blastn
[2023-06-13 16:48:26,524] [INFO] Selected 14 target genomes.
[2023-06-13 16:48:26,524] [INFO] Target genome list was writen to GCA_022708475.1_ASM2270847v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:48:26,532] [INFO] Task started: fastANI
[2023-06-13 16:48:26,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae077ce-5b81-4bce-aba4-16f165592348/GCA_022708475.1_ASM2270847v1_genomic.fna.gz --refList GCA_022708475.1_ASM2270847v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708475.1_ASM2270847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:48:33,738] [INFO] Task succeeded: fastANI
[2023-06-13 16:48:33,750] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:48:33,750] [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_018433525.1	s__MVYY01 sp002068215	99.2719	579	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__MVYY01	95.0	99.44	99.16	0.91	0.88	5	conclusive
GCA_012517575.1	s__MVYY01 sp012517575	85.5305	441	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__MVYY01	95.0	98.55	98.43	0.78	0.75	3	-
GCA_018056165.1	s__MVYY01 sp018056165	80.298	127	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__MVYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009929375.1	s__Paludibacter sp009929375	76.2497	57	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427615.1	s__Paludibacter sp002427615	75.9663	73	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.75	99.75	0.80	0.80	2	-
GCA_017882285.1	s__Paludibacter sp017882285	75.8422	59	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929065.1	s__Paludibacter sp903929065	75.7029	53	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:48:33,752] [INFO] GTDB search result was written to GCA_022708475.1_ASM2270847v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:48:33,753] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:48:33,756] [INFO] DFAST_QC result json was written to GCA_022708475.1_ASM2270847v1_genomic.fna/dqc_result.json
[2023-06-13 16:48:33,756] [INFO] DFAST_QC completed!
[2023-06-13 16:48:33,756] [INFO] Total running time: 0h1m11s