[2023-06-29 21:56:52,014] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:56:52,016] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:56:52,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference
[2023-06-29 21:56:53,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:56:53,228] [INFO] Task started: Prodigal
[2023-06-29 21:56:53,229] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ace940b-19aa-49fe-98a7-0230d704a66a/GCA_019414765.1_ASM1941476v1_genomic.fna.gz | prodigal -d GCA_019414765.1_ASM1941476v1_genomic.fna/cds.fna -a GCA_019414765.1_ASM1941476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:57:07,795] [INFO] Task succeeded: Prodigal
[2023-06-29 21:57:07,795] [INFO] Task started: HMMsearch
[2023-06-29 21:57:07,795] [INFO] Running command: hmmsearch --tblout GCA_019414765.1_ASM1941476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/reference_markers.hmm GCA_019414765.1_ASM1941476v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:57:08,048] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:57:08,050] [INFO] Found 6/6 markers.
[2023-06-29 21:57:08,078] [INFO] Query marker FASTA was written to GCA_019414765.1_ASM1941476v1_genomic.fna/markers.fasta
[2023-06-29 21:57:08,078] [INFO] Task started: Blastn
[2023-06-29 21:57:08,078] [INFO] Running command: blastn -query GCA_019414765.1_ASM1941476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/reference_markers.fasta -out GCA_019414765.1_ASM1941476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:57:08,698] [INFO] Task succeeded: Blastn
[2023-06-29 21:57:08,703] [INFO] Selected 16 target genomes.
[2023-06-29 21:57:08,703] [INFO] Target genome list was writen to GCA_019414765.1_ASM1941476v1_genomic.fna/target_genomes.txt
[2023-06-29 21:57:08,705] [INFO] Task started: fastANI
[2023-06-29 21:57:08,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ace940b-19aa-49fe-98a7-0230d704a66a/GCA_019414765.1_ASM1941476v1_genomic.fna.gz --refList GCA_019414765.1_ASM1941476v1_genomic.fna/target_genomes.txt --output GCA_019414765.1_ASM1941476v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:57:19,330] [INFO] Task succeeded: fastANI
[2023-06-29 21:57:19,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:57:19,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:57:19,356] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:57:19,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:57:19,357] [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 coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	82.995	658	1000	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	80.2048	294	1000	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	80.1105	299	1000	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	79.5679	308	1000	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.5563	327	1000	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.2582	305	1000	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.1558	312	1000	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	78.1535	178	1000	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.1528	240	1000	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	78.0507	180	1000	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.7676	180	1000	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	77.5933	122	1000	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.4773	117	1000	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	77.4755	138	1000	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.4468	124	1000	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.283	128	1000	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:57:19,359] [INFO] DFAST Taxonomy check result was written to GCA_019414765.1_ASM1941476v1_genomic.fna/tc_result.tsv
[2023-06-29 21:57:19,359] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:57:19,359] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:57:19,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/checkm_data
[2023-06-29 21:57:19,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:57:19,396] [INFO] Task started: CheckM
[2023-06-29 21:57:19,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019414765.1_ASM1941476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019414765.1_ASM1941476v1_genomic.fna/checkm_input GCA_019414765.1_ASM1941476v1_genomic.fna/checkm_result
[2023-06-29 21:58:04,391] [INFO] Task succeeded: CheckM
[2023-06-29 21:58:04,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:58:04,413] [INFO] ===== Completeness check finished =====
[2023-06-29 21:58:04,413] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:58:04,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019414765.1_ASM1941476v1_genomic.fna/markers.fasta)
[2023-06-29 21:58:04,414] [INFO] Task started: Blastn
[2023-06-29 21:58:04,414] [INFO] Running command: blastn -query GCA_019414765.1_ASM1941476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce50ede-aed1-4056-a412-da645814ce35/dqc_reference/reference_markers_gtdb.fasta -out GCA_019414765.1_ASM1941476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:58:05,278] [INFO] Task succeeded: Blastn
[2023-06-29 21:58:05,284] [INFO] Selected 14 target genomes.
[2023-06-29 21:58:05,284] [INFO] Target genome list was writen to GCA_019414765.1_ASM1941476v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:58:05,286] [INFO] Task started: fastANI
[2023-06-29 21:58:05,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ace940b-19aa-49fe-98a7-0230d704a66a/GCA_019414765.1_ASM1941476v1_genomic.fna.gz --refList GCA_019414765.1_ASM1941476v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019414765.1_ASM1941476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:58:14,140] [INFO] Task succeeded: fastANI
[2023-06-29 21:58:14,154] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:58:14,154] [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
GCA_000432735.1	s__Phocaeicola sp000432735	96.8963	800	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	conclusive
GCA_000436795.1	s__Phocaeicola sp000436795	88.6869	650	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_000154845.1	s__Phocaeicola coprocola	83.0205	657	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_003437535.1	s__Phocaeicola plebeius_A	81.0837	336	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_000157915.1	s__Phocaeicola coprophilus	80.1292	298	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	79.7913	293	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_900128495.1	s__Phocaeicola ilei	79.768	329	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	79.6542	311	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000187895.1	s__Phocaeicola plebeius	79.5763	307	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_013618865.1	s__Phocaeicola sp900541515	79.5576	328	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.547	234	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553185.1	s__Phocaeicola sp900553185	79.4916	200	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCF_000374585.1	s__Phocaeicola barnesiae	79.2646	305	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.1905	256	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:58:14,159] [INFO] GTDB search result was written to GCA_019414765.1_ASM1941476v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:58:14,160] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:58:14,164] [INFO] DFAST_QC result json was written to GCA_019414765.1_ASM1941476v1_genomic.fna/dqc_result.json
[2023-06-29 21:58:14,164] [INFO] DFAST_QC completed!
[2023-06-29 21:58:14,165] [INFO] Total running time: 0h1m22s