[2024-01-25 17:39:35,686] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference
[2024-01-25 17:39:36,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,782] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bf827e2-ea25-4394-b32c-f30cb83d87af/GCF_009495405.1_ASM949540v1_genomic.fna.gz | prodigal -d GCF_009495405.1_ASM949540v1_genomic.fna/cds.fna -a GCF_009495405.1_ASM949540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:50,715] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:50,716] [INFO] Task started: HMMsearch
[2024-01-25 17:39:50,716] [INFO] Running command: hmmsearch --tblout GCF_009495405.1_ASM949540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/reference_markers.hmm GCF_009495405.1_ASM949540v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:50,932] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:50,934] [INFO] Found 6/6 markers.
[2024-01-25 17:39:50,961] [INFO] Query marker FASTA was written to GCF_009495405.1_ASM949540v1_genomic.fna/markers.fasta
[2024-01-25 17:39:50,961] [INFO] Task started: Blastn
[2024-01-25 17:39:50,961] [INFO] Running command: blastn -query GCF_009495405.1_ASM949540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/reference_markers.fasta -out GCF_009495405.1_ASM949540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:51,520] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:51,522] [INFO] Selected 15 target genomes.
[2024-01-25 17:39:51,523] [INFO] Target genome list was writen to GCF_009495405.1_ASM949540v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:51,537] [INFO] Task started: fastANI
[2024-01-25 17:39:51,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf827e2-ea25-4394-b32c-f30cb83d87af/GCF_009495405.1_ASM949540v1_genomic.fna.gz --refList GCF_009495405.1_ASM949540v1_genomic.fna/target_genomes.txt --output GCF_009495405.1_ASM949540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:02,293] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:02,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:02,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:02,302] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:40:02,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:02,302] [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 copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	100.0	1058	1064	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	99.9713	1061	1064	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	99.9134	1011	1064	95	conclusive
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	83.8055	533	1064	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.4435	146	1064	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	78.06	119	1064	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.9887	119	1064	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	77.9846	119	1064	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	77.6571	106	1064	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	77.4747	83	1064	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.0287	77	1064	95	below_threshold
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	76.3418	52	1064	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	76.3313	51	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:02,303] [INFO] DFAST Taxonomy check result was written to GCF_009495405.1_ASM949540v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:02,304] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:02,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:02,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/checkm_data
[2024-01-25 17:40:02,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:02,340] [INFO] Task started: CheckM
[2024-01-25 17:40:02,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009495405.1_ASM949540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009495405.1_ASM949540v1_genomic.fna/checkm_input GCF_009495405.1_ASM949540v1_genomic.fna/checkm_result
[2024-01-25 17:40:43,886] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:43,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:43,904] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:43,905] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:43,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009495405.1_ASM949540v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:43,905] [INFO] Task started: Blastn
[2024-01-25 17:40:43,905] [INFO] Running command: blastn -query GCF_009495405.1_ASM949540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa32ec6-94e6-402b-9ab4-9790b87b453d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009495405.1_ASM949540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:44,790] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:44,792] [INFO] Selected 10 target genomes.
[2024-01-25 17:40:44,792] [INFO] Target genome list was writen to GCF_009495405.1_ASM949540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:44,805] [INFO] Task started: fastANI
[2024-01-25 17:40:44,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf827e2-ea25-4394-b32c-f30cb83d87af/GCF_009495405.1_ASM949540v1_genomic.fna.gz --refList GCF_009495405.1_ASM949540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009495405.1_ASM949540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:54,068] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:54,075] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 17:40:54,075] [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_000157935.1	s__Prevotella copri	99.9713	1061	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	inconclusive
GCF_015074785.1	s__Prevotella sp015074785	95.9512	817	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	inconclusive
GCF_019127135.1	s__Prevotella sp900551275	94.6511	804	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900557255.1	s__Prevotella sp900557255	94.0746	469	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009494395.1	s__Prevotella sp900546535	87.1657	703	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_019249655.1	s__Prevotella sp900767615	86.6714	698	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_002224675.1	s__Prevotella copri_A	86.5161	664	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900544825.1	s__Prevotella sp900544825	86.0617	629	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	85.7837	545	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900765465.1	s__Prevotella sp900765465	82.9428	316	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:54,076] [INFO] GTDB search result was written to GCF_009495405.1_ASM949540v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:54,077] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:54,080] [INFO] DFAST_QC result json was written to GCF_009495405.1_ASM949540v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:54,080] [INFO] DFAST_QC completed!
[2024-01-25 17:40:54,080] [INFO] Total running time: 0h1m18s