[2024-01-24 13:46:28,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:28,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:28,137] [INFO] DQC Reference Directory: /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference
[2024-01-24 13:46:29,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:29,344] [INFO] Task started: Prodigal
[2024-01-24 13:46:29,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg89dc58b8-2409-4d4a-b055-d6efaa9b45d6/GCF_000154845.1_ASM15484v1_genomic.fna.gz | prodigal -d GCF_000154845.1_ASM15484v1_genomic.fna/cds.fna -a GCF_000154845.1_ASM15484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:48,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:48,972] [INFO] Task started: HMMsearch
[2024-01-24 13:46:48,972] [INFO] Running command: hmmsearch --tblout GCF_000154845.1_ASM15484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/reference_markers.hmm GCF_000154845.1_ASM15484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:49,248] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:49,250] [INFO] Found 6/6 markers.
[2024-01-24 13:46:49,287] [INFO] Query marker FASTA was written to GCF_000154845.1_ASM15484v1_genomic.fna/markers.fasta
[2024-01-24 13:46:49,288] [INFO] Task started: Blastn
[2024-01-24 13:46:49,288] [INFO] Running command: blastn -query GCF_000154845.1_ASM15484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/reference_markers.fasta -out GCF_000154845.1_ASM15484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,926] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:49,927] [INFO] Target genome list was writen to GCF_000154845.1_ASM15484v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:49,973] [INFO] Task started: fastANI
[2024-01-24 13:46:49,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg89dc58b8-2409-4d4a-b055-d6efaa9b45d6/GCF_000154845.1_ASM15484v1_genomic.fna.gz --refList GCF_000154845.1_ASM15484v1_genomic.fna/target_genomes.txt --output GCF_000154845.1_ASM15484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:04,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:04,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:04,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:04,898] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:04,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:04,898] [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	100.0	1378	1387	95	conclusive
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	84.2943	244	1387	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	84.1448	444	1387	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	83.0609	186	1387	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	82.9913	186	1387	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	82.9252	178	1387	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	82.806	213	1387	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	82.3278	377	1387	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	80.7697	330	1387	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.751	325	1387	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	80.2562	158	1387	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.8243	142	1387	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.6525	333	1387	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.6452	320	1387	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.1627	258	1387	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.0026	192	1387	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.8652	249	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:04,900] [INFO] DFAST Taxonomy check result was written to GCF_000154845.1_ASM15484v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:04,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:04,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:04,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/checkm_data
[2024-01-24 13:47:04,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:04,944] [INFO] Task started: CheckM
[2024-01-24 13:47:04,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000154845.1_ASM15484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000154845.1_ASM15484v1_genomic.fna/checkm_input GCF_000154845.1_ASM15484v1_genomic.fna/checkm_result
[2024-01-24 13:48:01,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:01,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:02,012] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:02,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:02,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000154845.1_ASM15484v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:02,013] [INFO] Task started: Blastn
[2024-01-24 13:48:02,013] [INFO] Running command: blastn -query GCF_000154845.1_ASM15484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44b1a82-03e0-49b6-85f5-e5cee88817a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000154845.1_ASM15484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:02,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:02,896] [INFO] Selected 17 target genomes.
[2024-01-24 13:48:02,896] [INFO] Target genome list was writen to GCF_000154845.1_ASM15484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:02,934] [INFO] Task started: fastANI
[2024-01-24 13:48:02,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg89dc58b8-2409-4d4a-b055-d6efaa9b45d6/GCF_000154845.1_ASM15484v1_genomic.fna.gz --refList GCF_000154845.1_ASM15484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000154845.1_ASM15484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:15,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:15,660] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:15,660] [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_000154845.1	s__Phocaeicola coprocola	100.0	1379	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	conclusive
GCF_000187895.1	s__Phocaeicola plebeius	84.1096	445	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_000155815.1	s__Bacteroides eggerthii	82.9725	177	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCA_000432735.1	s__Phocaeicola sp000432735	82.9143	704	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_000436795.1	s__Phocaeicola sp000436795	82.6979	603	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_003437535.1	s__Phocaeicola plebeius_A	80.9768	355	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_000374585.1	s__Phocaeicola barnesiae	80.8275	326	1387	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	79.6954	303	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCF_000157915.1	s__Phocaeicola coprophilus	79.6845	330	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_900546645.1	s__Phocaeicola sp900546645	79.4411	257	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.94	98.88	0.79	0.75	3	-
GCF_016902295.1	s__Phocaeicola caecigallinarum_A	79.2052	260	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.48	97.48	0.83	0.83	2	-
GCA_000613385.1	s__Bacteroides acidifaciens	78.5564	170	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_016900695.1	s__Phocaeicola sp900540105	78.4987	240	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.97	98.76	0.92	0.88	6	-
GCA_900551645.1	s__Phocaeicola sp900551645	78.241	213	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_900546095.1	s__Phocaeicola excrementipullorum	77.5656	140	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.76	98.76	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:15,662] [INFO] GTDB search result was written to GCF_000154845.1_ASM15484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:15,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:15,666] [INFO] DFAST_QC result json was written to GCF_000154845.1_ASM15484v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:15,666] [INFO] DFAST_QC completed!
[2024-01-24 13:48:15,666] [INFO] Total running time: 0h1m48s