[2023-06-13 09:48:30,226] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:30,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:30,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference
[2023-06-13 09:48:31,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:31,431] [INFO] Task started: Prodigal
[2023-06-13 09:48:31,431] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9f8eeec-6c0a-4736-9507-fa1403d30c2f/GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:48:35,028] [INFO] Task succeeded: Prodigal
[2023-06-13 09:48:35,029] [INFO] Task started: HMMsearch
[2023-06-13 09:48:35,029] [INFO] Running command: hmmsearch --tblout GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/reference_markers.hmm GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:48:35,254] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:48:35,256] [INFO] Found 6/6 markers.
[2023-06-13 09:48:35,281] [INFO] Query marker FASTA was written to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 09:48:35,282] [INFO] Task started: Blastn
[2023-06-13 09:48:35,282] [INFO] Running command: blastn -query GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/reference_markers.fasta -out GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:48:35,862] [INFO] Task succeeded: Blastn
[2023-06-13 09:48:35,867] [INFO] Selected 17 target genomes.
[2023-06-13 09:48:35,868] [INFO] Target genome list was writen to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:48:35,926] [INFO] Task started: fastANI
[2023-06-13 09:48:35,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9f8eeec-6c0a-4736-9507-fa1403d30c2f/GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:48:41,425] [INFO] Task succeeded: fastANI
[2023-06-13 09:48:41,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:48:41,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:48:41,444] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:48:41,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:48:41,444] [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
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	78.902	88	497	95	below_threshold
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	78.5276	83	497	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	78.3261	93	497	95	below_threshold
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	78.2883	93	497	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	78.2043	84	497	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	78.1749	96	497	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	78.169	96	497	95	below_threshold
Veillonella denticariosi	strain=JCM 15641	GCA_002959855.1	419208	419208	type	True	78.109	68	497	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	78.0159	95	497	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	77.9619	68	497	95	below_threshold
Veillonella rodentium	strain=NCTC12018	GCA_900187285.1	248315	248315	type	True	77.7839	70	497	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	77.7767	102	497	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	77.762	99	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:48:41,447] [INFO] DFAST Taxonomy check result was written to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:48:41,447] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:48:41,447] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:48:41,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/checkm_data
[2023-06-13 09:48:41,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:48:41,468] [INFO] Task started: CheckM
[2023-06-13 09:48:41,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 09:48:59,375] [INFO] Task succeeded: CheckM
[2023-06-13 09:48:59,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:48:59,422] [INFO] ===== Completeness check finished =====
[2023-06-13 09:48:59,422] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:48:59,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:48:59,423] [INFO] Task started: Blastn
[2023-06-13 09:48:59,423] [INFO] Running command: blastn -query GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7022dffb-ac59-46e4-9e04-b4efd4adeac9/dqc_reference/reference_markers_gtdb.fasta -out GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:00,230] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:00,235] [INFO] Selected 17 target genomes.
[2023-06-13 09:49:00,236] [INFO] Target genome list was writen to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:49:00,246] [INFO] Task started: fastANI
[2023-06-13 09:49:00,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9f8eeec-6c0a-4736-9507-fa1403d30c2f/GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:06,616] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:06,632] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 09:49:06,633] [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_900550455.1	s__Veillonella sp900550455	97.2141	337	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.21	96.84	0.92	0.76	5	inconclusive
GCA_900549805.1	s__Veillonella sp900549805	95.0462	375	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_002959895.1	s__Veillonella infantium	78.8031	87	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCF_001078375.1	s__Veillonella tobetsuensis	78.5276	83	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCF_002959775.1	s__Veillonella rogosae	78.3261	93	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
GCF_013393365.1	s__Veillonella nakazawae	78.1749	96	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	-
GCF_003463825.1	s__Veillonella sp003463825	78.1375	100	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.70	95.41	0.92	0.86	3	-
GCA_009929605.1	s__Veillonella sp009929605	77.9393	68	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	99.43	99.31	0.85	0.82	7	-
GCF_900187285.1	s__Veillonella rodentium	77.7839	70	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.3196	N/A	N/A	N/A	N/A	1	-
GCF_900637515.1	s__Veillonella dispar	77.762	99	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCA_900538355.1	s__Veillonella sp900538355	77.6761	104	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214495.1	s__Veillonella sp905214495	76.8777	57	497	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:49:06,635] [INFO] GTDB search result was written to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:06,636] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:06,640] [INFO] DFAST_QC result json was written to GCA_938044065.1_ERR589696_bin.58_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:49:06,640] [INFO] DFAST_QC completed!
[2023-06-13 09:49:06,641] [INFO] Total running time: 0h0m36s