[2024-01-24 13:02:03,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference
[2024-01-24 13:02:05,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,007] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,008] [INFO] Running command: gunzip -c /var/lib/cwl/stge1381f60-2b08-4c22-baaa-97271068a954/GCF_000162875.1_ASM16287v1_genomic.fna.gz | prodigal -d GCF_000162875.1_ASM16287v1_genomic.fna/cds.fna -a GCF_000162875.1_ASM16287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:11,424] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:11,424] [INFO] Task started: HMMsearch
[2024-01-24 13:02:11,424] [INFO] Running command: hmmsearch --tblout GCF_000162875.1_ASM16287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/reference_markers.hmm GCF_000162875.1_ASM16287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:11,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:11,594] [INFO] Found 6/6 markers.
[2024-01-24 13:02:11,617] [INFO] Query marker FASTA was written to GCF_000162875.1_ASM16287v1_genomic.fna/markers.fasta
[2024-01-24 13:02:11,618] [INFO] Task started: Blastn
[2024-01-24 13:02:11,618] [INFO] Running command: blastn -query GCF_000162875.1_ASM16287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/reference_markers.fasta -out GCF_000162875.1_ASM16287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:12,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:12,232] [INFO] Selected 13 target genomes.
[2024-01-24 13:02:12,232] [INFO] Target genome list was writen to GCF_000162875.1_ASM16287v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:12,236] [INFO] Task started: fastANI
[2024-01-24 13:02:12,236] [INFO] Running command: fastANI --query /var/lib/cwl/stge1381f60-2b08-4c22-baaa-97271068a954/GCF_000162875.1_ASM16287v1_genomic.fna.gz --refList GCF_000162875.1_ASM16287v1_genomic.fna/target_genomes.txt --output GCF_000162875.1_ASM16287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:18,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:18,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:18,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:18,043] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:18,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:18,043] [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
Slackia exigua	strain=ATCC 700122	GCA_000162875.1	84109	84109	type	True	100.0	698	698	95	conclusive
Slackia exigua	strain=NCTC12994	GCA_900450505.1	84109	84109	type	True	99.9815	695	698	95	conclusive
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.5662	200	698	95	below_threshold
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	78.3277	133	698	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	78.1393	123	698	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	77.8443	121	698	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	77.8316	122	698	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	77.7858	117	698	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	77.774	174	698	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.7083	164	698	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.6587	165	698	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	77.4529	173	698	95	below_threshold
Raoultibacter massiliensis	strain=Marseille-P2849	GCA_900199545.1	1852371	1852371	type	True	77.317	110	698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:18,045] [INFO] DFAST Taxonomy check result was written to GCF_000162875.1_ASM16287v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:18,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:18,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:18,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/checkm_data
[2024-01-24 13:02:18,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:18,072] [INFO] Task started: CheckM
[2024-01-24 13:02:18,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000162875.1_ASM16287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000162875.1_ASM16287v1_genomic.fna/checkm_input GCF_000162875.1_ASM16287v1_genomic.fna/checkm_result
[2024-01-24 13:02:40,569] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:40,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,586] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:40,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:40,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000162875.1_ASM16287v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:40,587] [INFO] Task started: Blastn
[2024-01-24 13:02:40,587] [INFO] Running command: blastn -query GCF_000162875.1_ASM16287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc316c5f-5ed7-4bd1-9489-e50d75bd78ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000162875.1_ASM16287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:41,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:41,483] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:41,483] [INFO] Target genome list was writen to GCF_000162875.1_ASM16287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:41,497] [INFO] Task started: fastANI
[2024-01-24 13:02:41,497] [INFO] Running command: fastANI --query /var/lib/cwl/stge1381f60-2b08-4c22-baaa-97271068a954/GCF_000162875.1_ASM16287v1_genomic.fna.gz --refList GCF_000162875.1_ASM16287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000162875.1_ASM16287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:48,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:48,945] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:48,945] [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_000162875.1	s__Slackia exigua	100.0	698	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia	95.0	99.04	98.10	0.97	0.94	3	conclusive
GCF_003725295.1	s__Slackia_A faecicanis	78.5662	200	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814825.1	s__Berryella intestinalis	78.3921	135	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Berryella	95.0	96.96	96.96	0.86	0.86	2	-
GCF_011038975.1	s__CAAEEV01 sp011038975	78.2488	156	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003339845.1	s__Gordonibacter sp003339845	78.2225	143	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	78.1655	151	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_000296445.1	s__Slackia_A piriformis	78.0528	121	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.02	96.04	0.96	0.92	3	-
GCF_009911695.1	s__QWKK01 sp009911695	78.0477	126	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	98.01	97.98	0.92	0.92	3	-
GCA_900553775.1	s__Slackia_A sp900553775	77.9548	160	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCA_900555495.1	s__Slackia_A sp900555495	77.9423	121	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	100.00	100.00	0.96	0.96	2	-
GCA_013201155.1	s__Berryella sp013201155	77.7779	105	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Berryella	95.0	98.94	98.86	0.97	0.97	3	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	77.5594	118	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459925.1	s__UBA9715 sp017459925	77.5334	123	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754495.1	s__Aphodovivens avicola	77.5064	125	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	77.4378	63	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_910589695.1	s__QWKK01 sp910589695	77.4291	114	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589125.1	s__MGBC163016 sp910589125	76.818	74	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__MGBC163016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314535.1	s__UBA7748 sp900314535	76.4104	61	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	97.59	96.11	0.86	0.80	25	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:48,947] [INFO] GTDB search result was written to GCF_000162875.1_ASM16287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:48,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:48,952] [INFO] DFAST_QC result json was written to GCF_000162875.1_ASM16287v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:48,952] [INFO] DFAST_QC completed!
[2024-01-24 13:02:48,952] [INFO] Total running time: 0h0m45s