[2023-06-08 10:52:19,802] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:52:19,804] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:52:19,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference
[2023-06-08 10:52:21,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:52:21,046] [INFO] Task started: Prodigal
[2023-06-08 10:52:21,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dfac6e3-3bc9-4a66-bcb2-077e3e67e90d/GCA_945902955.1_MiH-14oct19-69_genomic.fna.gz | prodigal -d GCA_945902955.1_MiH-14oct19-69_genomic.fna/cds.fna -a GCA_945902955.1_MiH-14oct19-69_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:52:39,220] [INFO] Task succeeded: Prodigal
[2023-06-08 10:52:39,220] [INFO] Task started: HMMsearch
[2023-06-08 10:52:39,221] [INFO] Running command: hmmsearch --tblout GCA_945902955.1_MiH-14oct19-69_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/reference_markers.hmm GCA_945902955.1_MiH-14oct19-69_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:52:39,529] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:52:39,531] [INFO] Found 6/6 markers.
[2023-06-08 10:52:39,570] [INFO] Query marker FASTA was written to GCA_945902955.1_MiH-14oct19-69_genomic.fna/markers.fasta
[2023-06-08 10:52:39,571] [INFO] Task started: Blastn
[2023-06-08 10:52:39,571] [INFO] Running command: blastn -query GCA_945902955.1_MiH-14oct19-69_genomic.fna/markers.fasta -db /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/reference_markers.fasta -out GCA_945902955.1_MiH-14oct19-69_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:52:40,160] [INFO] Task succeeded: Blastn
[2023-06-08 10:52:40,165] [INFO] Selected 26 target genomes.
[2023-06-08 10:52:40,166] [INFO] Target genome list was writen to GCA_945902955.1_MiH-14oct19-69_genomic.fna/target_genomes.txt
[2023-06-08 10:52:40,201] [INFO] Task started: fastANI
[2023-06-08 10:52:40,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfac6e3-3bc9-4a66-bcb2-077e3e67e90d/GCA_945902955.1_MiH-14oct19-69_genomic.fna.gz --refList GCA_945902955.1_MiH-14oct19-69_genomic.fna/target_genomes.txt --output GCA_945902955.1_MiH-14oct19-69_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:52:54,897] [INFO] Task succeeded: fastANI
[2023-06-08 10:52:54,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:52:54,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:52:54,904] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:52:54,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:52:54,904] [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
Paludibacter propionicigenes	strain=WB4	GCA_000183135.1	185300	185300	type	True	77.1852	118	1371	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:52:54,907] [INFO] DFAST Taxonomy check result was written to GCA_945902955.1_MiH-14oct19-69_genomic.fna/tc_result.tsv
[2023-06-08 10:52:54,908] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:52:54,908] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:52:54,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/checkm_data
[2023-06-08 10:52:54,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:52:54,953] [INFO] Task started: CheckM
[2023-06-08 10:52:54,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945902955.1_MiH-14oct19-69_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945902955.1_MiH-14oct19-69_genomic.fna/checkm_input GCA_945902955.1_MiH-14oct19-69_genomic.fna/checkm_result
[2023-06-08 10:53:47,431] [INFO] Task succeeded: CheckM
[2023-06-08 10:53:47,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:53:47,454] [INFO] ===== Completeness check finished =====
[2023-06-08 10:53:47,454] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:53:47,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945902955.1_MiH-14oct19-69_genomic.fna/markers.fasta)
[2023-06-08 10:53:47,455] [INFO] Task started: Blastn
[2023-06-08 10:53:47,455] [INFO] Running command: blastn -query GCA_945902955.1_MiH-14oct19-69_genomic.fna/markers.fasta -db /var/lib/cwl/stgac9dab8b-06ea-433b-a28d-c73c8fd9dca7/dqc_reference/reference_markers_gtdb.fasta -out GCA_945902955.1_MiH-14oct19-69_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:53:48,257] [INFO] Task succeeded: Blastn
[2023-06-08 10:53:48,267] [INFO] Selected 18 target genomes.
[2023-06-08 10:53:48,267] [INFO] Target genome list was writen to GCA_945902955.1_MiH-14oct19-69_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:53:48,275] [INFO] Task started: fastANI
[2023-06-08 10:53:48,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfac6e3-3bc9-4a66-bcb2-077e3e67e90d/GCA_945902955.1_MiH-14oct19-69_genomic.fna.gz --refList GCA_945902955.1_MiH-14oct19-69_genomic.fna/target_genomes_gtdb.txt --output GCA_945902955.1_MiH-14oct19-69_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:53:59,401] [INFO] Task succeeded: fastANI
[2023-06-08 10:53:59,420] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 10:53:59,420] [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_903912795.1	s__Paludibacter sp903912795	79.6384	328	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911085.1	s__Paludibacter sp903911085	78.3556	246	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.87	0.95	0.95	3	-
GCA_017989795.1	s__Paludibacter sp017989795	78.1729	189	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873635.1	s__Paludibacter sp001873635	78.0068	194	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054805.1	s__Paludibacter sp018054805	77.7914	70	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937795.1	s__Paludibacter sp016937795	77.3429	155	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013426815.1	s__Paludibacter sp013426815	77.2427	137	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183135.1	s__Paludibacter propionicigenes	77.1767	116	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163375.1	s__Paludibacter sp019163375	77.0833	153	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830915.1	s__Paludibacter sp903830915	77.0497	129	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873355.1	s__Paludibacter sp903873355	77.0364	96	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882285.1	s__Paludibacter sp017882285	77.0156	121	1371	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	76.9434	140	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.75	99.75	0.80	0.80	2	-
GCA_010365115.1	s__Paludibacter sp010365115	76.8735	146	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654525.1	s__Paludibacter sp015654525	76.8093	104	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901975.1	s__Paludibacter sp903901975	76.6625	147	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.88	0.94	0.92	6	-
GCA_903929065.1	s__Paludibacter sp903929065	76.6536	116	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860345.1	s__Paludibacter sp017860345	76.4851	120	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:53:59,430] [INFO] GTDB search result was written to GCA_945902955.1_MiH-14oct19-69_genomic.fna/result_gtdb.tsv
[2023-06-08 10:53:59,431] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:53:59,436] [INFO] DFAST_QC result json was written to GCA_945902955.1_MiH-14oct19-69_genomic.fna/dqc_result.json
[2023-06-08 10:53:59,437] [INFO] DFAST_QC completed!
[2023-06-08 10:53:59,437] [INFO] Total running time: 0h1m40s