[2023-06-28 08:21:51,446] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:21:51,449] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:21:51,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference
[2023-06-28 08:21:55,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:21:55,114] [INFO] Task started: Prodigal
[2023-06-28 08:21:55,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c6380a4-8391-45b6-a516-59a53a2e0a16/GCA_017481925.1_ASM1748192v1_genomic.fna.gz | prodigal -d GCA_017481925.1_ASM1748192v1_genomic.fna/cds.fna -a GCA_017481925.1_ASM1748192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:22:05,863] [INFO] Task succeeded: Prodigal
[2023-06-28 08:22:05,863] [INFO] Task started: HMMsearch
[2023-06-28 08:22:05,863] [INFO] Running command: hmmsearch --tblout GCA_017481925.1_ASM1748192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/reference_markers.hmm GCA_017481925.1_ASM1748192v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:22:06,095] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:22:06,096] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c6380a4-8391-45b6-a516-59a53a2e0a16/GCA_017481925.1_ASM1748192v1_genomic.fna.gz]
[2023-06-28 08:22:06,122] [INFO] Query marker FASTA was written to GCA_017481925.1_ASM1748192v1_genomic.fna/markers.fasta
[2023-06-28 08:22:06,123] [INFO] Task started: Blastn
[2023-06-28 08:22:06,123] [INFO] Running command: blastn -query GCA_017481925.1_ASM1748192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/reference_markers.fasta -out GCA_017481925.1_ASM1748192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:06,709] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:06,713] [INFO] Selected 18 target genomes.
[2023-06-28 08:22:06,713] [INFO] Target genome list was writen to GCA_017481925.1_ASM1748192v1_genomic.fna/target_genomes.txt
[2023-06-28 08:22:06,715] [INFO] Task started: fastANI
[2023-06-28 08:22:06,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c6380a4-8391-45b6-a516-59a53a2e0a16/GCA_017481925.1_ASM1748192v1_genomic.fna.gz --refList GCA_017481925.1_ASM1748192v1_genomic.fna/target_genomes.txt --output GCA_017481925.1_ASM1748192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:22:19,767] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:19,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:22:19,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:22:19,778] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:22:19,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:22:19,778] [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
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.7825	86	596	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	76.6931	83	596	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	76.6519	56	596	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.5977	90	596	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.5316	91	596	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.5316	91	596	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.4133	92	596	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	76.3647	91	596	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:22:19,780] [INFO] DFAST Taxonomy check result was written to GCA_017481925.1_ASM1748192v1_genomic.fna/tc_result.tsv
[2023-06-28 08:22:19,781] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:22:19,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:22:19,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/checkm_data
[2023-06-28 08:22:19,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:22:19,815] [INFO] Task started: CheckM
[2023-06-28 08:22:19,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017481925.1_ASM1748192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017481925.1_ASM1748192v1_genomic.fna/checkm_input GCA_017481925.1_ASM1748192v1_genomic.fna/checkm_result
[2023-06-28 08:22:55,333] [INFO] Task succeeded: CheckM
[2023-06-28 08:22:55,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.01%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 08:22:55,359] [INFO] ===== Completeness check finished =====
[2023-06-28 08:22:55,359] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:22:55,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017481925.1_ASM1748192v1_genomic.fna/markers.fasta)
[2023-06-28 08:22:55,360] [INFO] Task started: Blastn
[2023-06-28 08:22:55,361] [INFO] Running command: blastn -query GCA_017481925.1_ASM1748192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg432c6931-7ae5-43eb-adf3-8e23481f0717/dqc_reference/reference_markers_gtdb.fasta -out GCA_017481925.1_ASM1748192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:56,194] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:56,198] [INFO] Selected 9 target genomes.
[2023-06-28 08:22:56,199] [INFO] Target genome list was writen to GCA_017481925.1_ASM1748192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:22:56,204] [INFO] Task started: fastANI
[2023-06-28 08:22:56,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c6380a4-8391-45b6-a516-59a53a2e0a16/GCA_017481925.1_ASM1748192v1_genomic.fna.gz --refList GCA_017481925.1_ASM1748192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017481925.1_ASM1748192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:22:59,963] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:59,972] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:22:59,973] [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_017481925.1	s__Alistipes sp017481925	100.0	593	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	96.75	96.65	0.89	0.83	5	conclusive
GCA_017391665.1	s__Alistipes sp017391665	86.6666	379	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.61	98.61	0.75	0.75	2	-
GCA_017628595.1	s__Alistipes sp017628595	85.3618	307	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.53	97.53	0.74	0.74	2	-
GCA_017631035.1	s__Alistipes sp017631035	82.901	286	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059925.1	s__Alistipes sp015059925	82.116	436	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.56	97.45	0.96	0.96	5	-
GCA_015059845.1	s__Alistipes sp015059845	81.6216	416	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.42	97.01	0.88	0.86	7	-
GCA_017380275.1	s__Alistipes sp017380275	80.9305	250	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017384185.1	s__Alistipes sp017384185	80.218	247	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060015.1	s__Alistipes sp015060015	79.3479	248	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:22:59,975] [INFO] GTDB search result was written to GCA_017481925.1_ASM1748192v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:22:59,975] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:22:59,979] [INFO] DFAST_QC result json was written to GCA_017481925.1_ASM1748192v1_genomic.fna/dqc_result.json
[2023-06-28 08:22:59,980] [INFO] DFAST_QC completed!
[2023-06-28 08:22:59,980] [INFO] Total running time: 0h1m9s