[2024-01-24 14:05:14,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:14,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:14,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference
[2024-01-24 14:05:15,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:15,650] [INFO] Task started: Prodigal
[2024-01-24 14:05:15,650] [INFO] Running command: gunzip -c /var/lib/cwl/stga2274433-9830-45f1-9a65-ee550cd2033e/GCF_900232875.1_PRJEB23011_genomic.fna.gz | prodigal -d GCF_900232875.1_PRJEB23011_genomic.fna/cds.fna -a GCF_900232875.1_PRJEB23011_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:32,535] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:32,536] [INFO] Task started: HMMsearch
[2024-01-24 14:05:32,536] [INFO] Running command: hmmsearch --tblout GCF_900232875.1_PRJEB23011_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/reference_markers.hmm GCF_900232875.1_PRJEB23011_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:32,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:32,790] [INFO] Found 6/6 markers.
[2024-01-24 14:05:32,823] [INFO] Query marker FASTA was written to GCF_900232875.1_PRJEB23011_genomic.fna/markers.fasta
[2024-01-24 14:05:32,824] [INFO] Task started: Blastn
[2024-01-24 14:05:32,824] [INFO] Running command: blastn -query GCF_900232875.1_PRJEB23011_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/reference_markers.fasta -out GCF_900232875.1_PRJEB23011_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:33,421] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:33,425] [INFO] Selected 19 target genomes.
[2024-01-24 14:05:33,426] [INFO] Target genome list was writen to GCF_900232875.1_PRJEB23011_genomic.fna/target_genomes.txt
[2024-01-24 14:05:33,467] [INFO] Task started: fastANI
[2024-01-24 14:05:33,468] [INFO] Running command: fastANI --query /var/lib/cwl/stga2274433-9830-45f1-9a65-ee550cd2033e/GCF_900232875.1_PRJEB23011_genomic.fna.gz --refList GCF_900232875.1_PRJEB23011_genomic.fna/target_genomes.txt --output GCF_900232875.1_PRJEB23011_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:47,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:47,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:47,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:47,588] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:47,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:47,588] [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 neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	80.9856	75	1262	95	below_threshold
Parabacteroides bouchesdurhonensis	strain=Marseille-P3763	GCA_900186615.1	1936995	1936995	type	True	80.1494	609	1262	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	79.6735	279	1262	95	below_threshold
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	79.5108	299	1262	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	79.4602	296	1262	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	79.3484	286	1262	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	79.2504	337	1262	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	79.1813	267	1262	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	79.1378	298	1262	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	79.1356	297	1262	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	78.8298	332	1262	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	78.8002	322	1262	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	78.7747	319	1262	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	78.7573	266	1262	95	below_threshold
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	78.6806	269	1262	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	78.5037	317	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:47,590] [INFO] DFAST Taxonomy check result was written to GCF_900232875.1_PRJEB23011_genomic.fna/tc_result.tsv
[2024-01-24 14:05:47,591] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:47,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:47,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/checkm_data
[2024-01-24 14:05:47,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:47,632] [INFO] Task started: CheckM
[2024-01-24 14:05:47,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900232875.1_PRJEB23011_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900232875.1_PRJEB23011_genomic.fna/checkm_input GCF_900232875.1_PRJEB23011_genomic.fna/checkm_result
[2024-01-24 14:06:38,476] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:38,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:38,499] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:38,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:38,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900232875.1_PRJEB23011_genomic.fna/markers.fasta)
[2024-01-24 14:06:38,501] [INFO] Task started: Blastn
[2024-01-24 14:06:38,501] [INFO] Running command: blastn -query GCF_900232875.1_PRJEB23011_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c4de886-4966-4e16-aea4-a14c0e966e90/dqc_reference/reference_markers_gtdb.fasta -out GCF_900232875.1_PRJEB23011_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:39,444] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:39,450] [INFO] Selected 21 target genomes.
[2024-01-24 14:06:39,451] [INFO] Target genome list was writen to GCF_900232875.1_PRJEB23011_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:39,474] [INFO] Task started: fastANI
[2024-01-24 14:06:39,474] [INFO] Running command: fastANI --query /var/lib/cwl/stga2274433-9830-45f1-9a65-ee550cd2033e/GCF_900232875.1_PRJEB23011_genomic.fna.gz --refList GCF_900232875.1_PRJEB23011_genomic.fna/target_genomes_gtdb.txt --output GCF_900232875.1_PRJEB23011_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:56,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,093] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:56,094] [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_900108035.1	s__Parabacteroides chinchillae	97.9159	1021	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	conclusive
GCF_000499785.1	s__Bacteroides neonati	81.0106	74	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900186615.1	s__Parabacteroides bouchesdurhonensis	80.1425	607	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.72	97.72	0.92	0.92	3	-
GCF_000969835.1	s__Parabacteroides goldsteinii	79.2941	338	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_014287585.1	s__Parabacteroides sp014287585	79.1037	290	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCF_003473295.1	s__Parabacteroides sp003473295	78.8526	317	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900128505.1	s__Parabacteroides timonensis	78.8392	332	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_000969825.1	s__Parabacteroides gordonii	78.7745	321	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_015550595.1	s__Parabacteroides sp900540715	78.7158	334	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_900155425.1	s__Parabacteroides massiliensis	78.6199	256	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCA_900760525.1	s__Parabacteroides sp900760525	78.536	249	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_910577325.1	s__Parabacteroides sp910577325	78.4814	220	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541965.1	s__Parabacteroides sp900541965	78.2688	288	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.98	99.95	0.94	0.89	3	-
GCA_905196875.1	s__Parabacteroides sp905196875	78.2317	275	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038785.1	s__Parabacteroides sp011038785	78.1947	162	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017560165.1	s__Parabacteroides sp017560165	78.1602	97	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	78.1278	186	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481945.1	s__Parabacteroides sp017481945	78.1246	155	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.47	98.47	0.80	0.80	2	-
GCF_900292045.1	s__Parabacteroides_B pacaensis	78.0375	149	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,095] [INFO] GTDB search result was written to GCF_900232875.1_PRJEB23011_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:56,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:56,100] [INFO] DFAST_QC result json was written to GCF_900232875.1_PRJEB23011_genomic.fna/dqc_result.json
[2024-01-24 14:06:56,101] [INFO] DFAST_QC completed!
[2024-01-24 14:06:56,101] [INFO] Total running time: 0h1m42s