[2023-06-30 21:00:32,005] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:00:32,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:00:32,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference
[2023-06-30 21:00:33,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:00:33,247] [INFO] Task started: Prodigal
[2023-06-30 21:00:33,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg27a4e6b8-b247-439b-89ef-a095a48763f1/GCA_900757645.1_ERS537345_3_genomic.fna.gz | prodigal -d GCA_900757645.1_ERS537345_3_genomic.fna/cds.fna -a GCA_900757645.1_ERS537345_3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:00:34,930] [INFO] Task succeeded: Prodigal
[2023-06-30 21:00:34,931] [INFO] Task started: HMMsearch
[2023-06-30 21:00:34,931] [INFO] Running command: hmmsearch --tblout GCA_900757645.1_ERS537345_3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/reference_markers.hmm GCA_900757645.1_ERS537345_3_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:00:35,088] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:00:35,089] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27a4e6b8-b247-439b-89ef-a095a48763f1/GCA_900757645.1_ERS537345_3_genomic.fna.gz]
[2023-06-30 21:00:35,137] [INFO] Query marker FASTA was written to GCA_900757645.1_ERS537345_3_genomic.fna/markers.fasta
[2023-06-30 21:00:35,137] [INFO] Task started: Blastn
[2023-06-30 21:00:35,137] [INFO] Running command: blastn -query GCA_900757645.1_ERS537345_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/reference_markers.fasta -out GCA_900757645.1_ERS537345_3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:00:35,705] [INFO] Task succeeded: Blastn
[2023-06-30 21:00:35,709] [INFO] Selected 25 target genomes.
[2023-06-30 21:00:35,709] [INFO] Target genome list was writen to GCA_900757645.1_ERS537345_3_genomic.fna/target_genomes.txt
[2023-06-30 21:00:35,712] [INFO] Task started: fastANI
[2023-06-30 21:00:35,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a4e6b8-b247-439b-89ef-a095a48763f1/GCA_900757645.1_ERS537345_3_genomic.fna.gz --refList GCA_900757645.1_ERS537345_3_genomic.fna/target_genomes.txt --output GCA_900757645.1_ERS537345_3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:00:46,653] [INFO] Task succeeded: fastANI
[2023-06-30 21:00:46,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:00:46,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:00:46,655] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:00:46,655] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:00:46,655] [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
--------------------------------------------------------------------------------
[2023-06-30 21:00:46,658] [INFO] DFAST Taxonomy check result was written to GCA_900757645.1_ERS537345_3_genomic.fna/tc_result.tsv
[2023-06-30 21:00:46,658] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:00:46,659] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:00:46,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/checkm_data
[2023-06-30 21:00:46,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:00:46,688] [INFO] Task started: CheckM
[2023-06-30 21:00:46,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900757645.1_ERS537345_3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900757645.1_ERS537345_3_genomic.fna/checkm_input GCA_900757645.1_ERS537345_3_genomic.fna/checkm_result
[2023-06-30 21:00:59,768] [INFO] Task succeeded: CheckM
[2023-06-30 21:00:59,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:00:59,788] [INFO] ===== Completeness check finished =====
[2023-06-30 21:00:59,788] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:00:59,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900757645.1_ERS537345_3_genomic.fna/markers.fasta)
[2023-06-30 21:00:59,789] [INFO] Task started: Blastn
[2023-06-30 21:00:59,789] [INFO] Running command: blastn -query GCA_900757645.1_ERS537345_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e9ac27-b83a-4a74-ba03-198fff4aa7f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_900757645.1_ERS537345_3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:01:00,581] [INFO] Task succeeded: Blastn
[2023-06-30 21:01:00,585] [INFO] Selected 23 target genomes.
[2023-06-30 21:01:00,586] [INFO] Target genome list was writen to GCA_900757645.1_ERS537345_3_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:01:00,589] [INFO] Task started: fastANI
[2023-06-30 21:01:00,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a4e6b8-b247-439b-89ef-a095a48763f1/GCA_900757645.1_ERS537345_3_genomic.fna.gz --refList GCA_900757645.1_ERS537345_3_genomic.fna/target_genomes_gtdb.txt --output GCA_900757645.1_ERS537345_3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:01:05,929] [INFO] Task succeeded: fastANI
[2023-06-30 21:01:05,946] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:01:05,946] [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_900550255.1	s__UBA5026 sp900550255	98.6544	311	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	conclusive
GCA_014845975.1	s__UBA5026 sp014845975	78.578	67	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936845.1	s__UBA5026 sp017936845	78.0143	127	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546745.1	s__UBA5026 sp900546745	77.9985	112	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.44	97.52	0.85	0.83	4	-
GCA_017940575.1	s__UBA5026 sp017940575	77.8578	71	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552335.1	s__UBA5026 sp900552335	77.8508	68	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.50	98.50	0.82	0.82	2	-
GCA_015059545.1	s__UBA5026 sp015059545	77.3943	131	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576795.1	s__UBA5026 sp910576795	77.3937	70	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584305.1	s__UBA5026 sp910584305	77.3358	90	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716405.1	s__Faecisoma merdavium	77.2951	86	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_900546275.1	s__UMGS872 sp900546275	77.2455	96	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	97.38	97.34	0.83	0.82	3	-
GCA_017476705.1	s__UBA5026 sp017476705	77.2221	79	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544605.1	s__SIG204 sp900544605	77.1757	84	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	98.54	98.50	0.89	0.86	3	-
GCA_000432255.1	s__Faecisoma sp000432255	77.1205	72	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_015059155.1	s__UMGS1613 sp015059155	77.0203	52	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461465.1	s__RGIG4266 sp017461465	76.9168	56	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547995.1	s__UMGS1045 sp900547995	76.8684	102	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536505.1	s__UMGS1613 sp017536505	76.7557	72	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215145.1	s__UMGS872 sp905215145	76.6433	52	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313725.1	s__UBA5026 sp900313725	76.3848	88	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	99.45	98.91	0.94	0.90	3	-
GCA_904502155.1	s__CAJGDV01 sp904502155	76.3058	64	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAJGDV01	95.0	98.87	97.74	0.85	0.70	3	-
--------------------------------------------------------------------------------
[2023-06-30 21:01:05,948] [INFO] GTDB search result was written to GCA_900757645.1_ERS537345_3_genomic.fna/result_gtdb.tsv
[2023-06-30 21:01:05,949] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:01:05,952] [INFO] DFAST_QC result json was written to GCA_900757645.1_ERS537345_3_genomic.fna/dqc_result.json
[2023-06-30 21:01:05,952] [INFO] DFAST_QC completed!
[2023-06-30 21:01:05,952] [INFO] Total running time: 0h0m34s