[2023-06-28 18:17:11,595] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:17:11,597] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:17:11,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference
[2023-06-28 18:17:13,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:17:13,012] [INFO] Task started: Prodigal
[2023-06-28 18:17:13,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg91aaa52a-36d2-44bf-98d3-0e2e842f9cc7/GCA_944320705.1_BRZ_SN_bin45_genomic.fna.gz | prodigal -d GCA_944320705.1_BRZ_SN_bin45_genomic.fna/cds.fna -a GCA_944320705.1_BRZ_SN_bin45_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:17:32,118] [INFO] Task succeeded: Prodigal
[2023-06-28 18:17:32,118] [INFO] Task started: HMMsearch
[2023-06-28 18:17:32,118] [INFO] Running command: hmmsearch --tblout GCA_944320705.1_BRZ_SN_bin45_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/reference_markers.hmm GCA_944320705.1_BRZ_SN_bin45_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:17:32,391] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:17:32,392] [INFO] Found 6/6 markers.
[2023-06-28 18:17:32,421] [INFO] Query marker FASTA was written to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/markers.fasta
[2023-06-28 18:17:32,421] [INFO] Task started: Blastn
[2023-06-28 18:17:32,422] [INFO] Running command: blastn -query GCA_944320705.1_BRZ_SN_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/reference_markers.fasta -out GCA_944320705.1_BRZ_SN_bin45_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:17:33,096] [INFO] Task succeeded: Blastn
[2023-06-28 18:17:33,101] [INFO] Selected 25 target genomes.
[2023-06-28 18:17:33,102] [INFO] Target genome list was writen to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/target_genomes.txt
[2023-06-28 18:17:33,103] [INFO] Task started: fastANI
[2023-06-28 18:17:33,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg91aaa52a-36d2-44bf-98d3-0e2e842f9cc7/GCA_944320705.1_BRZ_SN_bin45_genomic.fna.gz --refList GCA_944320705.1_BRZ_SN_bin45_genomic.fna/target_genomes.txt --output GCA_944320705.1_BRZ_SN_bin45_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:17:50,061] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:50,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:17:50,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:17:50,078] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:17:50,079] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:17:50,079] [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 uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.5307	339	1026	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	78.4981	340	1026	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.4923	327	1026	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	78.4809	335	1026	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.468	314	1026	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.4589	316	1026	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.4354	324	1026	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	78.3849	340	1026	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.3357	317	1026	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.3202	319	1026	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.2972	322	1026	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.1847	249	1026	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.174	279	1026	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.1021	282	1026	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	77.6862	116	1026	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	77.6294	118	1026	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	77.5343	147	1026	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	77.4918	214	1026	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	77.411	152	1026	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.2525	136	1026	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	76.971	177	1026	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2061	77	1026	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:17:50,081] [INFO] DFAST Taxonomy check result was written to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/tc_result.tsv
[2023-06-28 18:17:50,082] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:17:50,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:17:50,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/checkm_data
[2023-06-28 18:17:50,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:17:50,115] [INFO] Task started: CheckM
[2023-06-28 18:17:50,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320705.1_BRZ_SN_bin45_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320705.1_BRZ_SN_bin45_genomic.fna/checkm_input GCA_944320705.1_BRZ_SN_bin45_genomic.fna/checkm_result
[2023-06-28 18:18:42,726] [INFO] Task succeeded: CheckM
[2023-06-28 18:18:42,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:18:42,753] [INFO] ===== Completeness check finished =====
[2023-06-28 18:18:42,754] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:18:42,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320705.1_BRZ_SN_bin45_genomic.fna/markers.fasta)
[2023-06-28 18:18:42,755] [INFO] Task started: Blastn
[2023-06-28 18:18:42,755] [INFO] Running command: blastn -query GCA_944320705.1_BRZ_SN_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stg918c85f0-20a5-48dc-ab50-8f562b5e4d25/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320705.1_BRZ_SN_bin45_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:18:43,718] [INFO] Task succeeded: Blastn
[2023-06-28 18:18:43,724] [INFO] Selected 12 target genomes.
[2023-06-28 18:18:43,724] [INFO] Target genome list was writen to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:18:43,726] [INFO] Task started: fastANI
[2023-06-28 18:18:43,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg91aaa52a-36d2-44bf-98d3-0e2e842f9cc7/GCA_944320705.1_BRZ_SN_bin45_genomic.fna.gz --refList GCA_944320705.1_BRZ_SN_bin45_genomic.fna/target_genomes_gtdb.txt --output GCA_944320705.1_BRZ_SN_bin45_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:18:52,403] [INFO] Task succeeded: fastANI
[2023-06-28 18:18:52,419] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:18:52,420] [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_900128475.1	s__Bacteroides massiliensis	97.3658	918	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	conclusive
GCA_019116805.1	s__Bacteroides merdavium	87.0273	621	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	85.8559	695	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900108345.1	s__Bacteroides ndongoniae	80.9984	488	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_905201685.1	s__Bacteroides sp905201685	80.3469	230	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553815.1	s__Bacteroides sp900553815	79.9399	360	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_018883785.1	s__Bacteroides intestinipullorum	78.8202	301	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	78.4802	327	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.3726	263	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_000154525.1	s__Bacteroides stercoris	78.32	319	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCA_905203765.1	s__Bacteroides sp905203765	78.0076	257	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	77.9345	216	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
--------------------------------------------------------------------------------
[2023-06-28 18:18:52,422] [INFO] GTDB search result was written to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/result_gtdb.tsv
[2023-06-28 18:18:52,422] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:18:52,440] [INFO] DFAST_QC result json was written to GCA_944320705.1_BRZ_SN_bin45_genomic.fna/dqc_result.json
[2023-06-28 18:18:52,441] [INFO] DFAST_QC completed!
[2023-06-28 18:18:52,441] [INFO] Total running time: 0h1m41s