[2023-06-28 07:34:11,158] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:34:11,159] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:34:11,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference
[2023-06-28 07:34:12,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:34:12,386] [INFO] Task started: Prodigal
[2023-06-28 07:34:12,386] [INFO] Running command: gunzip -c /var/lib/cwl/stg94347603-a2b1-41a8-a09d-6b72ac7b1892/GCA_017993145.1_ASM1799314v1_genomic.fna.gz | prodigal -d GCA_017993145.1_ASM1799314v1_genomic.fna/cds.fna -a GCA_017993145.1_ASM1799314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:35:01,129] [INFO] Task succeeded: Prodigal
[2023-06-28 07:35:01,130] [INFO] Task started: HMMsearch
[2023-06-28 07:35:01,130] [INFO] Running command: hmmsearch --tblout GCA_017993145.1_ASM1799314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/reference_markers.hmm GCA_017993145.1_ASM1799314v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:35:01,268] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:35:01,269] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg94347603-a2b1-41a8-a09d-6b72ac7b1892/GCA_017993145.1_ASM1799314v1_genomic.fna.gz]
[2023-06-28 07:35:01,282] [INFO] Query marker FASTA was written to GCA_017993145.1_ASM1799314v1_genomic.fna/markers.fasta
[2023-06-28 07:35:01,282] [INFO] Task started: Blastn
[2023-06-28 07:35:01,283] [INFO] Running command: blastn -query GCA_017993145.1_ASM1799314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/reference_markers.fasta -out GCA_017993145.1_ASM1799314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:35:01,762] [INFO] Task succeeded: Blastn
[2023-06-28 07:35:01,765] [INFO] Selected 10 target genomes.
[2023-06-28 07:35:01,765] [INFO] Target genome list was writen to GCA_017993145.1_ASM1799314v1_genomic.fna/target_genomes.txt
[2023-06-28 07:35:01,766] [INFO] Task started: fastANI
[2023-06-28 07:35:01,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg94347603-a2b1-41a8-a09d-6b72ac7b1892/GCA_017993145.1_ASM1799314v1_genomic.fna.gz --refList GCA_017993145.1_ASM1799314v1_genomic.fna/target_genomes.txt --output GCA_017993145.1_ASM1799314v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:35:08,698] [INFO] Task succeeded: fastANI
[2023-06-28 07:35:08,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:35:08,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:35:08,707] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 07:35:08,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 07:35:08,708] [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
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	98.861	315	322	95	conclusive
Bacteroides graminisolvens	strain=JCM 15093	GCA_000613825.1	477666	477666	type	True	98.8271	320	322	95	conclusive
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	78.5701	79	322	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	78.2249	59	322	95	below_threshold
Bacteroides ihuae	strain=Marseille-P2824	GCA_900104585.1	1852362	1852362	type	True	78.1411	120	322	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.979	64	322	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	77.9415	75	322	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	77.8339	81	322	95	below_threshold
Bacteroides reticulotermitis	strain=JCM 10512	GCA_000517545.1	1133319	1133319	type	True	77.6399	62	322	95	below_threshold
Bacteroides reticulotermitis	strain=DSM 105720	GCA_014196955.1	1133319	1133319	type	True	77.5361	65	322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:35:08,709] [INFO] DFAST Taxonomy check result was written to GCA_017993145.1_ASM1799314v1_genomic.fna/tc_result.tsv
[2023-06-28 07:35:08,710] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:35:08,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:35:08,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/checkm_data
[2023-06-28 07:35:08,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:35:08,723] [INFO] Task started: CheckM
[2023-06-28 07:35:08,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017993145.1_ASM1799314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017993145.1_ASM1799314v1_genomic.fna/checkm_input GCA_017993145.1_ASM1799314v1_genomic.fna/checkm_result
[2023-06-28 07:35:28,204] [INFO] Task succeeded: CheckM
[2023-06-28 07:35:28,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:35:28,217] [INFO] ===== Completeness check finished =====
[2023-06-28 07:35:28,218] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:35:28,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017993145.1_ASM1799314v1_genomic.fna/markers.fasta)
[2023-06-28 07:35:28,218] [INFO] Task started: Blastn
[2023-06-28 07:35:28,218] [INFO] Running command: blastn -query GCA_017993145.1_ASM1799314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fa60533-d366-4f0a-9bb0-4107f7e274db/dqc_reference/reference_markers_gtdb.fasta -out GCA_017993145.1_ASM1799314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:35:28,701] [INFO] Task succeeded: Blastn
[2023-06-28 07:35:28,704] [INFO] Selected 12 target genomes.
[2023-06-28 07:35:28,705] [INFO] Target genome list was writen to GCA_017993145.1_ASM1799314v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:35:28,707] [INFO] Task started: fastANI
[2023-06-28 07:35:28,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg94347603-a2b1-41a8-a09d-6b72ac7b1892/GCA_017993145.1_ASM1799314v1_genomic.fna.gz --refList GCA_017993145.1_ASM1799314v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017993145.1_ASM1799314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:35:37,069] [INFO] Task succeeded: fastANI
[2023-06-28 07:35:37,078] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:35:37,079] [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
GCF_000428125.1	s__Bacteroides graminisolvens	98.861	315	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	97.75	0.90	0.81	13	conclusive
GCF_000381365.1	s__Bacteroides salyersiae	78.5701	79	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_900130125.1	s__Bacteroides congonensis	78.2249	59	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_900104585.1	s__Bacteroides ihuae	78.1411	120	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307035.1	s__Bacteroides sp002307035	78.0032	111	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.69	98.69	0.85	0.85	2	-
GCF_000499785.1	s__Bacteroides neonati	77.9415	75	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903181435.1	s__Bacteroides sp900765785	77.7935	71	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_902364365.1	s__Bacteroides sp900556215	77.7411	61	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000517545.1	s__Bacteroides reticulotermitis	77.6399	62	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_900766195.1	s__Bacteroides sp900766195	77.1295	51	322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:35:37,081] [INFO] GTDB search result was written to GCA_017993145.1_ASM1799314v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:35:37,081] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:35:37,084] [INFO] DFAST_QC result json was written to GCA_017993145.1_ASM1799314v1_genomic.fna/dqc_result.json
[2023-06-28 07:35:37,084] [INFO] DFAST_QC completed!
[2023-06-28 07:35:37,085] [INFO] Total running time: 0h1m26s