[2023-06-08 08:48:56,239] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:48:56,242] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:48:56,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference
[2023-06-08 08:48:57,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:48:57,671] [INFO] Task started: Prodigal
[2023-06-08 08:48:57,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e24aa02-459e-40e6-b56f-b69ca94f397e/GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:49:03,303] [INFO] Task succeeded: Prodigal
[2023-06-08 08:49:03,304] [INFO] Task started: HMMsearch
[2023-06-08 08:49:03,304] [INFO] Running command: hmmsearch --tblout GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/reference_markers.hmm GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:49:03,594] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:49:03,595] [INFO] Found 6/6 markers.
[2023-06-08 08:49:03,632] [INFO] Query marker FASTA was written to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:49:03,633] [INFO] Task started: Blastn
[2023-06-08 08:49:03,633] [INFO] Running command: blastn -query GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/reference_markers.fasta -out GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:04,400] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:04,404] [INFO] Selected 8 target genomes.
[2023-06-08 08:49:04,405] [INFO] Target genome list was writen to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:49:04,406] [INFO] Task started: fastANI
[2023-06-08 08:49:04,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e24aa02-459e-40e6-b56f-b69ca94f397e/GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:49:08,905] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:08,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:49:08,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:49:08,915] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:49:08,916] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:49:08,916] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	80.3396	322	588	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	80.2323	334	588	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.5571	175	588	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.5089	177	588	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.169	192	588	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.8032	124	588	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.1911	145	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:49:08,918] [INFO] DFAST Taxonomy check result was written to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:49:08,919] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:49:08,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:49:08,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/checkm_data
[2023-06-08 08:49:08,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:49:08,945] [INFO] Task started: CheckM
[2023-06-08 08:49:08,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:49:31,893] [INFO] Task succeeded: CheckM
[2023-06-08 08:49:31,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:49:31,915] [INFO] ===== Completeness check finished =====
[2023-06-08 08:49:31,915] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:49:31,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:49:31,916] [INFO] Task started: Blastn
[2023-06-08 08:49:31,916] [INFO] Running command: blastn -query GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e9262f-759d-473f-a54a-8f5dfb5f7fec/dqc_reference/reference_markers_gtdb.fasta -out GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:33,109] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:33,114] [INFO] Selected 8 target genomes.
[2023-06-08 08:49:33,114] [INFO] Target genome list was writen to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:49:33,116] [INFO] Task started: fastANI
[2023-06-08 08:49:33,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e24aa02-459e-40e6-b56f-b69ca94f397e/GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:49:37,854] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:37,869] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:49:37,869] [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_900554145.1	s__Gemmiger sp900554145	98.2295	453	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.15	98.15	0.80	0.80	2	conclusive
GCA_900540595.1	s__Gemmiger sp900540595	85.9083	478	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.09	95.97	0.86	0.82	4	-
GCF_900167555.1	s__Gemmiger formicilis	85.734	494	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.67	96.73	0.89	0.78	43	-
GCF_018784445.1	s__Gemmiger sp900540775	85.5206	509	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.04	97.97	0.87	0.81	8	-
GCA_900539695.1	s__Gemmiger sp900539695	82.3441	403	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.42	97.91	0.86	0.79	8	-
GCA_004554775.1	s__Gemmiger variabilis_B	81.6778	444	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.40	97.89	0.89	0.88	3	-
GCA_004552305.1	s__Gemmiger variabilis_A	81.5076	364	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.82	96.59	0.82	0.70	4	-
GCA_900545545.1	s__Gemmiger sp900545545	80.5629	325	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	96.26	96.20	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-08 08:49:37,872] [INFO] GTDB search result was written to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:49:37,872] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:49:37,877] [INFO] DFAST_QC result json was written to GCA_945910295.1_SRR11489782_bin.3_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:49:37,878] [INFO] DFAST_QC completed!
[2023-06-08 08:49:37,878] [INFO] Total running time: 0h0m42s