[2023-06-05 07:16:05,777] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:05,779] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:05,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference
[2023-06-05 07:16:07,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:07,189] [INFO] Task started: Prodigal
[2023-06-05 07:16:07,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg34fbb347-2953-4831-9233-2416abdd9b6d/GCA_004559005.1_ASM455900v1_genomic.fna.gz | prodigal -d GCA_004559005.1_ASM455900v1_genomic.fna/cds.fna -a GCA_004559005.1_ASM455900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:13,338] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:13,339] [INFO] Task started: HMMsearch
[2023-06-05 07:16:13,339] [INFO] Running command: hmmsearch --tblout GCA_004559005.1_ASM455900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/reference_markers.hmm GCA_004559005.1_ASM455900v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:13,564] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:13,565] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg34fbb347-2953-4831-9233-2416abdd9b6d/GCA_004559005.1_ASM455900v1_genomic.fna.gz]
[2023-06-05 07:16:13,589] [INFO] Query marker FASTA was written to GCA_004559005.1_ASM455900v1_genomic.fna/markers.fasta
[2023-06-05 07:16:13,589] [INFO] Task started: Blastn
[2023-06-05 07:16:13,589] [INFO] Running command: blastn -query GCA_004559005.1_ASM455900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/reference_markers.fasta -out GCA_004559005.1_ASM455900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:14,251] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:14,255] [INFO] Selected 17 target genomes.
[2023-06-05 07:16:14,255] [INFO] Target genome list was writen to GCA_004559005.1_ASM455900v1_genomic.fna/target_genomes.txt
[2023-06-05 07:16:14,258] [INFO] Task started: fastANI
[2023-06-05 07:16:14,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fbb347-2953-4831-9233-2416abdd9b6d/GCA_004559005.1_ASM455900v1_genomic.fna.gz --refList GCA_004559005.1_ASM455900v1_genomic.fna/target_genomes.txt --output GCA_004559005.1_ASM455900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:22,302] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:22,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:22,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:22,315] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:22,315] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:16:22,315] [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
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	80.1042	223	573	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	79.5654	226	573	95	below_threshold
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	79.1662	234	573	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	78.8028	234	573	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	78.7344	208	573	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	78.6958	207	573	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	78.5876	227	573	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	78.523	216	573	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	78.3999	224	573	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	78.3964	236	573	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	78.3129	233	573	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	77.792	130	573	95	below_threshold
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	77.7724	141	573	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	77.0851	84	573	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	76.8987	57	573	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:16:22,317] [INFO] DFAST Taxonomy check result was written to GCA_004559005.1_ASM455900v1_genomic.fna/tc_result.tsv
[2023-06-05 07:16:22,318] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:22,319] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:22,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/checkm_data
[2023-06-05 07:16:22,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:22,350] [INFO] Task started: CheckM
[2023-06-05 07:16:22,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004559005.1_ASM455900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004559005.1_ASM455900v1_genomic.fna/checkm_input GCA_004559005.1_ASM455900v1_genomic.fna/checkm_result
[2023-06-05 07:16:47,352] [INFO] Task succeeded: CheckM
[2023-06-05 07:16:47,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.93%
Contamintation: 14.81%
Strain heterogeneity: 7.84%
--------------------------------------------------------------------------------
[2023-06-05 07:16:47,379] [INFO] ===== Completeness check finished =====
[2023-06-05 07:16:47,379] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:16:47,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004559005.1_ASM455900v1_genomic.fna/markers.fasta)
[2023-06-05 07:16:47,380] [INFO] Task started: Blastn
[2023-06-05 07:16:47,380] [INFO] Running command: blastn -query GCA_004559005.1_ASM455900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ba65415-9cd0-4aa1-b629-ce68992f92ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_004559005.1_ASM455900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:48,384] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:48,389] [INFO] Selected 16 target genomes.
[2023-06-05 07:16:48,389] [INFO] Target genome list was writen to GCA_004559005.1_ASM455900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:16:48,435] [INFO] Task started: fastANI
[2023-06-05 07:16:48,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fbb347-2953-4831-9233-2416abdd9b6d/GCA_004559005.1_ASM455900v1_genomic.fna.gz --refList GCA_004559005.1_ASM455900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004559005.1_ASM455900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:16:55,947] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:55,965] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:16:55,965] [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_008831035.1	s__Ellagibacter isourolithinifaciens	96.5806	485	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	96.52	96.27	0.85	0.76	13	conclusive
GCA_900554945.1	s__Ellagibacter sp900554945	93.6754	318	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236865.1	s__Senegalimassilia anaerobia	80.0786	224	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.57	95.07	0.88	0.81	7	-
GCF_000210055.1	s__Gordonibacter pamelaeae	79.5654	226	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCA_905215325.1	s__Senegalimassilia sp905215325	79.3766	206	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550055.1	s__Senegalimassilia sp900550055	79.3484	178	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	97.04	96.58	0.76	0.72	3	-
GCA_900754955.1	s__CAAEEV01 sp900754955	79.2137	176	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	79.0238	221	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_011038975.1	s__CAAEEV01 sp011038975	78.8116	225	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009834925.2	s__Eggerthella sp014287365	78.7918	234	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCA_900170005.1	s__Gordonibacter massiliensis	78.7079	233	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_902386925.1	s__Arabia massiliensis	78.6664	216	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900184265.1	s__Eggerthella timonensis	78.572	228	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339845.1	s__Gordonibacter sp003339845	78.5517	235	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900754495.1	s__Aphodovivens avicola	78.2475	165	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	-
GCF_003725955.1	s__Slackia_A isoflavoniconvertens	78.0384	109	573	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	-
--------------------------------------------------------------------------------
[2023-06-05 07:16:55,967] [INFO] GTDB search result was written to GCA_004559005.1_ASM455900v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:16:55,968] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:16:55,972] [INFO] DFAST_QC result json was written to GCA_004559005.1_ASM455900v1_genomic.fna/dqc_result.json
[2023-06-05 07:16:55,972] [INFO] DFAST_QC completed!
[2023-06-05 07:16:55,972] [INFO] Total running time: 0h0m50s