[2023-06-28 00:40:57,485] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:40:57,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:40:57,487] [INFO] DQC Reference Directory: /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference
[2023-06-28 00:40:58,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:40:58,767] [INFO] Task started: Prodigal
[2023-06-28 00:40:58,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aaa2a77-e8b1-4e1c-9a75-664073fd4a73/GCA_017541085.1_ASM1754108v1_genomic.fna.gz | prodigal -d GCA_017541085.1_ASM1754108v1_genomic.fna/cds.fna -a GCA_017541085.1_ASM1754108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:41:12,613] [INFO] Task succeeded: Prodigal
[2023-06-28 00:41:12,613] [INFO] Task started: HMMsearch
[2023-06-28 00:41:12,613] [INFO] Running command: hmmsearch --tblout GCA_017541085.1_ASM1754108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/reference_markers.hmm GCA_017541085.1_ASM1754108v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:41:12,907] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:41:12,909] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9aaa2a77-e8b1-4e1c-9a75-664073fd4a73/GCA_017541085.1_ASM1754108v1_genomic.fna.gz]
[2023-06-28 00:41:12,933] [INFO] Query marker FASTA was written to GCA_017541085.1_ASM1754108v1_genomic.fna/markers.fasta
[2023-06-28 00:41:12,933] [INFO] Task started: Blastn
[2023-06-28 00:41:12,933] [INFO] Running command: blastn -query GCA_017541085.1_ASM1754108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/reference_markers.fasta -out GCA_017541085.1_ASM1754108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:13,561] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:13,565] [INFO] Selected 19 target genomes.
[2023-06-28 00:41:13,565] [INFO] Target genome list was writen to GCA_017541085.1_ASM1754108v1_genomic.fna/target_genomes.txt
[2023-06-28 00:41:13,567] [INFO] Task started: fastANI
[2023-06-28 00:41:13,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaa2a77-e8b1-4e1c-9a75-664073fd4a73/GCA_017541085.1_ASM1754108v1_genomic.fna.gz --refList GCA_017541085.1_ASM1754108v1_genomic.fna/target_genomes.txt --output GCA_017541085.1_ASM1754108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:41:25,539] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:25,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:41:25,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:41:25,545] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:41:25,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:41:25,545] [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
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.6749	79	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:41:25,547] [INFO] DFAST Taxonomy check result was written to GCA_017541085.1_ASM1754108v1_genomic.fna/tc_result.tsv
[2023-06-28 00:41:25,548] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:41:25,548] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:41:25,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/checkm_data
[2023-06-28 00:41:25,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:41:25,586] [INFO] Task started: CheckM
[2023-06-28 00:41:25,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017541085.1_ASM1754108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017541085.1_ASM1754108v1_genomic.fna/checkm_input GCA_017541085.1_ASM1754108v1_genomic.fna/checkm_result
[2023-06-28 00:42:08,915] [INFO] Task succeeded: CheckM
[2023-06-28 00:42:08,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:42:08,936] [INFO] ===== Completeness check finished =====
[2023-06-28 00:42:08,936] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:42:08,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017541085.1_ASM1754108v1_genomic.fna/markers.fasta)
[2023-06-28 00:42:08,937] [INFO] Task started: Blastn
[2023-06-28 00:42:08,937] [INFO] Running command: blastn -query GCA_017541085.1_ASM1754108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga60ca4c1-2231-4a8d-bc27-6f29669255ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_017541085.1_ASM1754108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:42:09,826] [INFO] Task succeeded: Blastn
[2023-06-28 00:42:09,830] [INFO] Selected 19 target genomes.
[2023-06-28 00:42:09,830] [INFO] Target genome list was writen to GCA_017541085.1_ASM1754108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:42:09,838] [INFO] Task started: fastANI
[2023-06-28 00:42:09,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaa2a77-e8b1-4e1c-9a75-664073fd4a73/GCA_017541085.1_ASM1754108v1_genomic.fna.gz --refList GCA_017541085.1_ASM1754108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017541085.1_ASM1754108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:42:17,865] [INFO] Task succeeded: fastANI
[2023-06-28 00:42:17,891] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:42:17,892] [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_002373375.1	s__Prevotella sp002373375	95.1401	561	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.88	95.14	0.78	0.66	9	conclusive
GCA_002392645.1	s__Prevotella sp002392645	82.7861	284	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.38	96.38	0.66	0.66	2	-
GCA_016281055.1	s__Prevotella sp016281055	80.2149	326	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642485.1	s__Prevotella sp017642485	78.6583	112	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353585.1	s__Prevotella sp002353585	78.26	148	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.91	95.27	0.85	0.76	8	-
GCA_905233245.1	s__Prevotella sp905233245	78.1565	138	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.81	0.80	0.79	3	-
GCA_017541365.1	s__Prevotella sp017541365	77.8609	105	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065145.1	s__Prevotella sp018065145	77.7883	124	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478025.1	s__Prevotella sp017478025	77.6402	135	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.24	95.24	0.74	0.74	2	-
GCA_017479675.1	s__Prevotella sp017479675	77.5637	130	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.13	0.63	0.60	3	-
GCA_902799455.1	s__Prevotella sp902799455	77.2816	88	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233165.1	s__Prevotella sp905233165	77.1602	97	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475005.1	s__Prevotella sp017475005	77.1487	84	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.77	0.88	0.88	2	-
GCA_017623655.1	s__Prevotella sp017623655	76.7554	89	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552965.1	s__Prevotella sp900552965	76.3952	64	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.78	99.78	0.83	0.83	2	-
GCA_017415455.1	s__Prevotella sp017415455	76.2181	53	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_900548195.1	s__Prevotella sp900548195	76.0585	71	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.71	95.27	0.80	0.75	7	-
--------------------------------------------------------------------------------
[2023-06-28 00:42:17,894] [INFO] GTDB search result was written to GCA_017541085.1_ASM1754108v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:42:17,894] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:42:17,898] [INFO] DFAST_QC result json was written to GCA_017541085.1_ASM1754108v1_genomic.fna/dqc_result.json
[2023-06-28 00:42:17,899] [INFO] DFAST_QC completed!
[2023-06-28 00:42:17,899] [INFO] Total running time: 0h1m20s