[2024-01-24 12:07:06,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference
[2024-01-24 12:07:07,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,660] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg29c0656a-cd35-4d1b-ad78-7219d263fcd0/GCF_019973315.1_ASM1997331v1_genomic.fna.gz | prodigal -d GCF_019973315.1_ASM1997331v1_genomic.fna/cds.fna -a GCF_019973315.1_ASM1997331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:27,048] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:27,048] [INFO] Task started: HMMsearch
[2024-01-24 12:07:27,049] [INFO] Running command: hmmsearch --tblout GCF_019973315.1_ASM1997331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/reference_markers.hmm GCF_019973315.1_ASM1997331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:27,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:27,348] [INFO] Found 6/6 markers.
[2024-01-24 12:07:27,395] [INFO] Query marker FASTA was written to GCF_019973315.1_ASM1997331v1_genomic.fna/markers.fasta
[2024-01-24 12:07:27,396] [INFO] Task started: Blastn
[2024-01-24 12:07:27,396] [INFO] Running command: blastn -query GCF_019973315.1_ASM1997331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/reference_markers.fasta -out GCF_019973315.1_ASM1997331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:27,990] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:27,994] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:27,995] [INFO] Target genome list was writen to GCF_019973315.1_ASM1997331v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:28,003] [INFO] Task started: fastANI
[2024-01-24 12:07:28,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c0656a-cd35-4d1b-ad78-7219d263fcd0/GCF_019973315.1_ASM1997331v1_genomic.fna.gz --refList GCF_019973315.1_ASM1997331v1_genomic.fna/target_genomes.txt --output GCF_019973315.1_ASM1997331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:38,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:38,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:38,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:38,736] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:38,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:38,736] [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
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	100.0	1130	1130	95	conclusive
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	99.9674	1119	1130	95	conclusive
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	79.9316	67	1130	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	78.6091	185	1130	95	below_threshold
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	78.488	60	1130	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.4203	64	1130	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	78.0128	163	1130	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.7452	76	1130	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.7375	159	1130	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.5214	122	1130	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.4292	160	1130	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.2164	100	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:38,738] [INFO] DFAST Taxonomy check result was written to GCF_019973315.1_ASM1997331v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:38,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:38,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:38,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/checkm_data
[2024-01-24 12:07:38,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:38,773] [INFO] Task started: CheckM
[2024-01-24 12:07:38,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019973315.1_ASM1997331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019973315.1_ASM1997331v1_genomic.fna/checkm_input GCF_019973315.1_ASM1997331v1_genomic.fna/checkm_result
[2024-01-24 12:08:36,278] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:36,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:36,298] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:36,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:36,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019973315.1_ASM1997331v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:36,299] [INFO] Task started: Blastn
[2024-01-24 12:08:36,299] [INFO] Running command: blastn -query GCF_019973315.1_ASM1997331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d5375a-e9f2-4e99-9bd3-92c180256e4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019973315.1_ASM1997331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:37,133] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:37,137] [INFO] Selected 19 target genomes.
[2024-01-24 12:08:37,137] [INFO] Target genome list was writen to GCF_019973315.1_ASM1997331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:37,154] [INFO] Task started: fastANI
[2024-01-24 12:08:37,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c0656a-cd35-4d1b-ad78-7219d263fcd0/GCF_019973315.1_ASM1997331v1_genomic.fna.gz --refList GCF_019973315.1_ASM1997331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019973315.1_ASM1997331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:46,901] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:46,919] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:46,919] [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_000218235.1	s__Prevotella multisaccharivorax	99.9674	1119	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.48	98.36	0.88	0.83	3	conclusive
GCA_002353825.1	s__Prevotella sp002353825	80.0811	377	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.40	98.85	0.91	0.85	4	-
GCA_902792635.1	s__Prevotella sp902792635	79.5459	376	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.91	0.91	2	-
GCA_900315955.1	s__Prevotella sp900315955	79.0717	319	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	96.92	0.82	0.74	16	-
GCA_002299635.1	s__Prevotella sp002299635	78.8454	155	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.50	98.47	0.80	0.78	3	-
GCA_900546345.1	s__Prevotella sp900546345	78.4794	148	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002437565.1	s__Prevotella sp002437565	78.4719	201	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.98	98.57	0.78	0.73	8	-
GCA_900543585.1	s__Prevotella sp900543585	78.2275	195	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.73	96.00	0.84	0.76	4	-
GCA_900319905.1	s__Prevotella sp900319905	77.647	207	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.44	0.89	0.87	7	-
GCA_002481295.1	s__Prevotella sp002481295	77.3186	166	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_900762125.1	s__Prevotella sp900762125	77.3098	132	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431975.1	s__Prevotella sp000431975	77.1426	97	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.89	99.89	0.92	0.91	3	-
GCA_002437115.1	s__Prevotella sp002437115	76.8356	96	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765585.1	s__Prevotella sp902765585	76.0983	55	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801375.1	s__Prevotella sp902801375	76.0121	66	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
GCA_017417465.1	s__Prevotella sp017417465	75.9747	57	1130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:46,920] [INFO] GTDB search result was written to GCF_019973315.1_ASM1997331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:46,921] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:46,925] [INFO] DFAST_QC result json was written to GCF_019973315.1_ASM1997331v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:46,925] [INFO] DFAST_QC completed!
[2024-01-24 12:08:46,925] [INFO] Total running time: 0h1m41s