[2023-06-04 18:59:07,672] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:59:07,730] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:59:07,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference
[2023-06-04 18:59:10,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:59:10,196] [INFO] Task started: Prodigal
[2023-06-04 18:59:10,197] [INFO] Running command: gunzip -c /var/lib/cwl/stg42d43596-f73c-4b71-ae39-eeb491e69ab6/GCA_934644985.1_ERR7738173_bin.70_genomic.fna.gz | prodigal -d GCA_934644985.1_ERR7738173_bin.70_genomic.fna/cds.fna -a GCA_934644985.1_ERR7738173_bin.70_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:59:16,483] [INFO] Task succeeded: Prodigal
[2023-06-04 18:59:16,483] [INFO] Task started: HMMsearch
[2023-06-04 18:59:16,484] [INFO] Running command: hmmsearch --tblout GCA_934644985.1_ERR7738173_bin.70_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/reference_markers.hmm GCA_934644985.1_ERR7738173_bin.70_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:59:16,704] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:59:16,706] [INFO] Found 6/6 markers.
[2023-06-04 18:59:16,734] [INFO] Query marker FASTA was written to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/markers.fasta
[2023-06-04 18:59:16,735] [INFO] Task started: Blastn
[2023-06-04 18:59:16,735] [INFO] Running command: blastn -query GCA_934644985.1_ERR7738173_bin.70_genomic.fna/markers.fasta -db /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/reference_markers.fasta -out GCA_934644985.1_ERR7738173_bin.70_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:59:17,496] [INFO] Task succeeded: Blastn
[2023-06-04 18:59:17,501] [INFO] Selected 17 target genomes.
[2023-06-04 18:59:17,502] [INFO] Target genome list was writen to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/target_genomes.txt
[2023-06-04 18:59:17,508] [INFO] Task started: fastANI
[2023-06-04 18:59:17,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d43596-f73c-4b71-ae39-eeb491e69ab6/GCA_934644985.1_ERR7738173_bin.70_genomic.fna.gz --refList GCA_934644985.1_ERR7738173_bin.70_genomic.fna/target_genomes.txt --output GCA_934644985.1_ERR7738173_bin.70_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:59:26,333] [INFO] Task succeeded: fastANI
[2023-06-04 18:59:26,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:59:26,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:59:26,363] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:59:26,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:59:26,365] [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
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	80.8851	356	703	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	80.1384	358	703	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	80.1078	361	703	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	80.0287	343	703	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	79.9997	363	703	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	79.901	330	703	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	79.8973	333	703	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	79.8403	331	703	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	79.8171	335	703	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	79.809	331	703	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	79.8056	340	703	95	below_threshold
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	78.9179	239	703	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	78.6998	237	703	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	78.6886	228	703	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	78.6345	228	703	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	78.5604	247	703	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:59:26,368] [INFO] DFAST Taxonomy check result was written to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/tc_result.tsv
[2023-06-04 18:59:26,369] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:59:26,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:59:26,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/checkm_data
[2023-06-04 18:59:26,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:59:26,405] [INFO] Task started: CheckM
[2023-06-04 18:59:26,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934644985.1_ERR7738173_bin.70_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934644985.1_ERR7738173_bin.70_genomic.fna/checkm_input GCA_934644985.1_ERR7738173_bin.70_genomic.fna/checkm_result
[2023-06-04 18:59:49,819] [INFO] Task succeeded: CheckM
[2023-06-04 18:59:49,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:59:49,838] [INFO] ===== Completeness check finished =====
[2023-06-04 18:59:49,838] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:59:49,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934644985.1_ERR7738173_bin.70_genomic.fna/markers.fasta)
[2023-06-04 18:59:49,839] [INFO] Task started: Blastn
[2023-06-04 18:59:49,839] [INFO] Running command: blastn -query GCA_934644985.1_ERR7738173_bin.70_genomic.fna/markers.fasta -db /var/lib/cwl/stg059e807c-d748-49ce-b44c-feb56692dbcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934644985.1_ERR7738173_bin.70_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:59:51,125] [INFO] Task succeeded: Blastn
[2023-06-04 18:59:51,130] [INFO] Selected 16 target genomes.
[2023-06-04 18:59:51,131] [INFO] Target genome list was writen to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:59:51,184] [INFO] Task started: fastANI
[2023-06-04 18:59:51,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d43596-f73c-4b71-ae39-eeb491e69ab6/GCA_934644985.1_ERR7738173_bin.70_genomic.fna.gz --refList GCA_934644985.1_ERR7738173_bin.70_genomic.fna/target_genomes_gtdb.txt --output GCA_934644985.1_ERR7738173_bin.70_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:00:00,678] [INFO] Task succeeded: fastANI
[2023-06-04 19:00:00,696] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:00:00,697] [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_900754495.1	s__Aphodovivens avicola	96.4197	469	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	conclusive
GCA_900550385.1	s__Aphodovivens sp900550385	85.7117	407	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
GCA_018710945.1	s__Aphodovivens avistercoris	84.0113	487	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754955.1	s__CAAEEV01 sp900754955	81.0965	285	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCF_000210055.1	s__Gordonibacter pamelaeae	80.9028	355	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCA_018715935.1	s__Aphodovivens excrementavium	80.5561	336	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902386925.1	s__Arabia massiliensis	80.3901	349	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009911695.1	s__QWKK01 sp009911695	80.1951	255	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	98.01	97.98	0.92	0.92	3	-
GCF_002899695.1	s__Rubneribacter badeniensis	80.1951	308	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Rubneribacter	95.0	98.61	97.86	0.90	0.82	6	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	80.0848	363	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCA_900170005.1	s__Gordonibacter massiliensis	80.0479	359	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_900184265.1	s__Eggerthella timonensis	80.0387	342	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834925.2	s__Eggerthella sp014287365	79.9797	364	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_003339815.1	s__Eggerthella sinensis	79.9107	331	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCF_002159915.1	s__Rubneribacter sp002159915	79.7042	282	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Rubneribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	79.4791	251	703	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:00:00,699] [INFO] GTDB search result was written to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/result_gtdb.tsv
[2023-06-04 19:00:00,700] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:00:00,704] [INFO] DFAST_QC result json was written to GCA_934644985.1_ERR7738173_bin.70_genomic.fna/dqc_result.json
[2023-06-04 19:00:00,704] [INFO] DFAST_QC completed!
[2023-06-04 19:00:00,704] [INFO] Total running time: 0h0m53s