[2023-06-19 10:55:51,826] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:55:51,829] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:55:51,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference
[2023-06-19 10:55:53,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:55:53,291] [INFO] Task started: Prodigal
[2023-06-19 10:55:53,291] [INFO] Running command: gunzip -c /var/lib/cwl/stgca6e0c88-6fd8-4dba-97a3-1c65c45050c4/GCA_018376815.1_ASM1837681v1_genomic.fna.gz | prodigal -d GCA_018376815.1_ASM1837681v1_genomic.fna/cds.fna -a GCA_018376815.1_ASM1837681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:11,104] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:11,104] [INFO] Task started: HMMsearch
[2023-06-19 10:56:11,105] [INFO] Running command: hmmsearch --tblout GCA_018376815.1_ASM1837681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/reference_markers.hmm GCA_018376815.1_ASM1837681v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:11,393] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:11,394] [INFO] Found 6/6 markers.
[2023-06-19 10:56:11,429] [INFO] Query marker FASTA was written to GCA_018376815.1_ASM1837681v1_genomic.fna/markers.fasta
[2023-06-19 10:56:11,429] [INFO] Task started: Blastn
[2023-06-19 10:56:11,429] [INFO] Running command: blastn -query GCA_018376815.1_ASM1837681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/reference_markers.fasta -out GCA_018376815.1_ASM1837681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:12,074] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:12,079] [INFO] Selected 13 target genomes.
[2023-06-19 10:56:12,080] [INFO] Target genome list was writen to GCA_018376815.1_ASM1837681v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:12,083] [INFO] Task started: fastANI
[2023-06-19 10:56:12,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6e0c88-6fd8-4dba-97a3-1c65c45050c4/GCA_018376815.1_ASM1837681v1_genomic.fna.gz --refList GCA_018376815.1_ASM1837681v1_genomic.fna/target_genomes.txt --output GCA_018376815.1_ASM1837681v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:23,495] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:23,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:23,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:23,515] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 10:56:23,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 10:56:23,516] [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
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	98.0997	929	1111	95	conclusive
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	98.0889	922	1111	95	conclusive
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.9252	362	1111	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	79.6674	368	1111	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	79.5449	291	1111	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.252	361	1111	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.0903	365	1111	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.4677	240	1111	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.1166	139	1111	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.793	156	1111	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.7746	212	1111	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	77.7319	177	1111	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	77.3934	148	1111	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:56:23,519] [INFO] DFAST Taxonomy check result was written to GCA_018376815.1_ASM1837681v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:23,520] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:23,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:23,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/checkm_data
[2023-06-19 10:56:23,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:23,558] [INFO] Task started: CheckM
[2023-06-19 10:56:23,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376815.1_ASM1837681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376815.1_ASM1837681v1_genomic.fna/checkm_input GCA_018376815.1_ASM1837681v1_genomic.fna/checkm_result
[2023-06-19 10:57:15,625] [INFO] Task succeeded: CheckM
[2023-06-19 10:57:15,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:57:15,654] [INFO] ===== Completeness check finished =====
[2023-06-19 10:57:15,654] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:57:15,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376815.1_ASM1837681v1_genomic.fna/markers.fasta)
[2023-06-19 10:57:15,655] [INFO] Task started: Blastn
[2023-06-19 10:57:15,655] [INFO] Running command: blastn -query GCA_018376815.1_ASM1837681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d51dee-10ad-4f17-9d29-1349aaaaae5e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376815.1_ASM1837681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:57:16,540] [INFO] Task succeeded: Blastn
[2023-06-19 10:57:16,545] [INFO] Selected 17 target genomes.
[2023-06-19 10:57:16,546] [INFO] Target genome list was writen to GCA_018376815.1_ASM1837681v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:57:16,577] [INFO] Task started: fastANI
[2023-06-19 10:57:16,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6e0c88-6fd8-4dba-97a3-1c65c45050c4/GCA_018376815.1_ASM1837681v1_genomic.fna.gz --refList GCA_018376815.1_ASM1837681v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376815.1_ASM1837681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:26,728] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:26,746] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:57:26,746] [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_000374585.1	s__Phocaeicola barnesiae	98.0997	929	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	conclusive
GCA_900551645.1	s__Phocaeicola sp900551645	89.6018	560	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_900553185.1	s__Phocaeicola sp900553185	84.0083	495	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	80.2743	417	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	80.1869	399	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_013618865.1	s__Phocaeicola sp900541515	79.9138	362	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_003437535.1	s__Phocaeicola plebeius_A	79.8672	366	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_000187895.1	s__Phocaeicola plebeius	79.6674	368	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_900551445.1	s__Phocaeicola sp900551445	79.6487	312	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCF_900128495.1	s__Phocaeicola ilei	79.5717	361	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.5028	290	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.0524	239	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_000432735.1	s__Phocaeicola sp000432735	79.0258	331	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCF_016899805.1	s__Phocaeicola gallinaceus	78.3905	245	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.20	97.80	0.80	0.74	12	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.1173	237	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_004558305.1	s__Phocaeicola plebeius_B	77.7275	207	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120125.1	s__Phocaeicola excrementigallinarum	77.7136	256	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:26,749] [INFO] GTDB search result was written to GCA_018376815.1_ASM1837681v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:26,749] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:26,753] [INFO] DFAST_QC result json was written to GCA_018376815.1_ASM1837681v1_genomic.fna/dqc_result.json
[2023-06-19 10:57:26,753] [INFO] DFAST_QC completed!
[2023-06-19 10:57:26,753] [INFO] Total running time: 0h1m35s