[2023-06-30 14:54:27,838] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:54:27,841] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:54:27,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference
[2023-06-30 14:54:29,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:54:29,082] [INFO] Task started: Prodigal
[2023-06-30 14:54:29,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg07b92a29-ea15-4193-a75a-7b3bf09f958c/GCA_019409885.1_ASM1940988v1_genomic.fna.gz | prodigal -d GCA_019409885.1_ASM1940988v1_genomic.fna/cds.fna -a GCA_019409885.1_ASM1940988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:46,372] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:46,373] [INFO] Task started: HMMsearch
[2023-06-30 14:54:46,373] [INFO] Running command: hmmsearch --tblout GCA_019409885.1_ASM1940988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/reference_markers.hmm GCA_019409885.1_ASM1940988v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:46,629] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:46,631] [INFO] Found 6/6 markers.
[2023-06-30 14:54:46,677] [INFO] Query marker FASTA was written to GCA_019409885.1_ASM1940988v1_genomic.fna/markers.fasta
[2023-06-30 14:54:46,678] [INFO] Task started: Blastn
[2023-06-30 14:54:46,678] [INFO] Running command: blastn -query GCA_019409885.1_ASM1940988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/reference_markers.fasta -out GCA_019409885.1_ASM1940988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:47,288] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:47,293] [INFO] Selected 21 target genomes.
[2023-06-30 14:54:47,294] [INFO] Target genome list was writen to GCA_019409885.1_ASM1940988v1_genomic.fna/target_genomes.txt
[2023-06-30 14:54:47,296] [INFO] Task started: fastANI
[2023-06-30 14:54:47,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b92a29-ea15-4193-a75a-7b3bf09f958c/GCA_019409885.1_ASM1940988v1_genomic.fna.gz --refList GCA_019409885.1_ASM1940988v1_genomic.fna/target_genomes.txt --output GCA_019409885.1_ASM1940988v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:58,980] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:58,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:58,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:58,999] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:58,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:54:58,999] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	83.0771	424	954	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	81.8723	451	954	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	81.8186	428	954	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	81.8039	445	954	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	81.6551	179	954	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	78.3313	101	954	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	78.0909	117	954	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	77.8875	113	954	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	77.8427	119	954	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.7422	169	954	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	77.3381	61	954	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	77.2655	105	954	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	77.2554	76	954	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.2445	156	954	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	77.1358	67	954	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.0528	99	954	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.0272	145	954	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	77.0261	74	954	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.8709	109	954	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:54:59,001] [INFO] DFAST Taxonomy check result was written to GCA_019409885.1_ASM1940988v1_genomic.fna/tc_result.tsv
[2023-06-30 14:54:59,002] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:59,002] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:59,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/checkm_data
[2023-06-30 14:54:59,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:59,040] [INFO] Task started: CheckM
[2023-06-30 14:54:59,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019409885.1_ASM1940988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019409885.1_ASM1940988v1_genomic.fna/checkm_input GCA_019409885.1_ASM1940988v1_genomic.fna/checkm_result
[2023-06-30 14:55:50,266] [INFO] Task succeeded: CheckM
[2023-06-30 14:55:50,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:55:50,288] [INFO] ===== Completeness check finished =====
[2023-06-30 14:55:50,288] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:55:50,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019409885.1_ASM1940988v1_genomic.fna/markers.fasta)
[2023-06-30 14:55:50,289] [INFO] Task started: Blastn
[2023-06-30 14:55:50,289] [INFO] Running command: blastn -query GCA_019409885.1_ASM1940988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e98ba8a-0560-4cf7-96e7-f69ff27d2430/dqc_reference/reference_markers_gtdb.fasta -out GCA_019409885.1_ASM1940988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:55:51,151] [INFO] Task succeeded: Blastn
[2023-06-30 14:55:51,155] [INFO] Selected 16 target genomes.
[2023-06-30 14:55:51,156] [INFO] Target genome list was writen to GCA_019409885.1_ASM1940988v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:55:51,167] [INFO] Task started: fastANI
[2023-06-30 14:55:51,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b92a29-ea15-4193-a75a-7b3bf09f958c/GCA_019409885.1_ASM1940988v1_genomic.fna.gz --refList GCA_019409885.1_ASM1940988v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019409885.1_ASM1940988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:56:02,402] [INFO] Task succeeded: fastANI
[2023-06-30 14:56:02,418] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:56:02,418] [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_009495355.1	s__Prevotella sp900313215	96.8446	718	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	conclusive
GCA_900556395.1	s__Prevotella sp900556395	86.3313	520	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.81	0.83	0.82	3	-
GCA_002439605.1	s__Prevotella sp002439605	84.6549	504	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCF_004535825.1	s__Prevotella hominis	83.1136	423	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	-
GCF_009494395.1	s__Prevotella sp900546535	82.0169	439	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCF_015074785.1	s__Prevotella sp015074785	81.9029	449	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000157935.1	s__Prevotella copri	81.861	452	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900554835.1	s__Prevotella sp900554835	81.8099	371	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249655.1	s__Prevotella sp900767615	81.5291	453	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_900551985.1	s__Prevotella sp900551985	81.341	371	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_000436035.1	s__Prevotella sp000436035	80.4781	352	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCA_900555035.1	s__Prevotella sp900555035	80.4725	348	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451555.1	s__Prevotella sp002451555	80.3885	353	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCA_900548535.1	s__Prevotella sp900548535	80.288	382	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297965.1	s__Prevotella sp002297965	80.0706	321	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.14	99.14	0.78	0.78	2	-
GCA_900765465.1	s__Prevotella sp900765465	78.7479	211	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:56:02,420] [INFO] GTDB search result was written to GCA_019409885.1_ASM1940988v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:56:02,421] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:56:02,426] [INFO] DFAST_QC result json was written to GCA_019409885.1_ASM1940988v1_genomic.fna/dqc_result.json
[2023-06-30 14:56:02,426] [INFO] DFAST_QC completed!
[2023-06-30 14:56:02,426] [INFO] Total running time: 0h1m35s