[2024-01-24 10:57:20,782] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:20,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:20,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference
[2024-01-24 10:57:22,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,073] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf7b8d41-9666-4bbf-a206-85b381df13f7/GCF_900241005.1_PRJEB22714_genomic.fna.gz | prodigal -d GCF_900241005.1_PRJEB22714_genomic.fna/cds.fna -a GCF_900241005.1_PRJEB22714_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:41,034] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:41,034] [INFO] Task started: HMMsearch
[2024-01-24 10:57:41,034] [INFO] Running command: hmmsearch --tblout GCF_900241005.1_PRJEB22714_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/reference_markers.hmm GCF_900241005.1_PRJEB22714_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:41,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:41,315] [INFO] Found 6/6 markers.
[2024-01-24 10:57:41,348] [INFO] Query marker FASTA was written to GCF_900241005.1_PRJEB22714_genomic.fna/markers.fasta
[2024-01-24 10:57:41,349] [INFO] Task started: Blastn
[2024-01-24 10:57:41,349] [INFO] Running command: blastn -query GCF_900241005.1_PRJEB22714_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/reference_markers.fasta -out GCF_900241005.1_PRJEB22714_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,961] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,964] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:41,965] [INFO] Target genome list was writen to GCF_900241005.1_PRJEB22714_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,973] [INFO] Task started: fastANI
[2024-01-24 10:57:41,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b8d41-9666-4bbf-a206-85b381df13f7/GCF_900241005.1_PRJEB22714_genomic.fna.gz --refList GCF_900241005.1_PRJEB22714_genomic.fna/target_genomes.txt --output GCF_900241005.1_PRJEB22714_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,699] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,719] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,720] [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 cutis	strain=Marseille-P4118	GCA_900241005.1	2024197	2024197	type	True	100.0	1286	1288	95	conclusive
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	81.9624	573	1288	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	80.9122	533	1288	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	80.9035	540	1288	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	80.8678	541	1288	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	80.2051	479	1288	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	80.2023	489	1288	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.1935	498	1288	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	80.1639	497	1288	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	80.1576	474	1288	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	80.0071	521	1288	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	79.9732	504	1288	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	79.9694	519	1288	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	79.9523	463	1288	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	79.7369	456	1288	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.7301	450	1288	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	79.7147	467	1288	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	79.3608	434	1288	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	79.2759	466	1288	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	78.9264	452	1288	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	78.8813	272	1288	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	78.8285	443	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,732] [INFO] DFAST Taxonomy check result was written to GCF_900241005.1_PRJEB22714_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/checkm_data
[2024-01-24 10:58:01,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,785] [INFO] Task started: CheckM
[2024-01-24 10:58:01,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900241005.1_PRJEB22714_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900241005.1_PRJEB22714_genomic.fna/checkm_input GCF_900241005.1_PRJEB22714_genomic.fna/checkm_result
[2024-01-24 10:58:57,512] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:57,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:57,532] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:57,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:57,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900241005.1_PRJEB22714_genomic.fna/markers.fasta)
[2024-01-24 10:58:57,533] [INFO] Task started: Blastn
[2024-01-24 10:58:57,533] [INFO] Running command: blastn -query GCF_900241005.1_PRJEB22714_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e33260-95b3-47a1-83e2-e024c8b18bbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900241005.1_PRJEB22714_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:58,315] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:58,318] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:58,319] [INFO] Target genome list was writen to GCF_900241005.1_PRJEB22714_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:58,329] [INFO] Task started: fastANI
[2024-01-24 10:58:58,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b8d41-9666-4bbf-a206-85b381df13f7/GCF_900241005.1_PRJEB22714_genomic.fna.gz --refList GCF_900241005.1_PRJEB22714_genomic.fna/target_genomes_gtdb.txt --output GCF_900241005.1_PRJEB22714_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:13,464] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:13,477] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:13,478] [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_900241005.1	s__Bacteroides cutis	100.0	1286	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.53	99.47	0.92	0.89	5	conclusive
GCF_000155815.1	s__Bacteroides eggerthii	80.9053	534	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_003438615.1	s__Bacteroides sp003545565	80.4976	538	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000154205.1	s__Bacteroides uniformis	80.2343	484	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000154525.1	s__Bacteroides stercoris	80.1526	498	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCA_905215345.1	s__Bacteroides sp905215345	80.0166	566	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	80.0071	521	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000195635.1	s__Bacteroides fluxus	79.9732	504	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000614125.1	s__Bacteroides rodentium	79.9546	462	1288	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	79.7369	456	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_902388495.1	s__Bacteroides sp902388495	79.6991	415	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000172175.1	s__Bacteroides intestinalis	79.2816	465	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.18	96.30	0.86	0.76	22	-
GCA_900555635.1	s__Bacteroides sp900555635	79.1256	454	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
GCF_902364365.1	s__Bacteroides sp900556215	79.0498	450	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_003464595.1	s__Bacteroides intestinalis_A	78.9666	439	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	78.9226	453	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
GCF_000513195.1	s__Bacteroides timonensis	78.8514	440	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:13,479] [INFO] GTDB search result was written to GCF_900241005.1_PRJEB22714_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:13,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:13,486] [INFO] DFAST_QC result json was written to GCF_900241005.1_PRJEB22714_genomic.fna/dqc_result.json
[2024-01-24 10:59:13,487] [INFO] DFAST_QC completed!
[2024-01-24 10:59:13,487] [INFO] Total running time: 0h1m53s