[2023-06-13 02:55:00,064] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:55:00,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:55:00,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference
[2023-06-13 02:55:01,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:55:01,281] [INFO] Task started: Prodigal
[2023-06-13 02:55:01,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg20013480-db8f-4a5f-8b31-0770bde58d78/GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna.gz | prodigal -d GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/cds.fna -a GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:55:19,878] [INFO] Task succeeded: Prodigal
[2023-06-13 02:55:19,879] [INFO] Task started: HMMsearch
[2023-06-13 02:55:19,879] [INFO] Running command: hmmsearch --tblout GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/reference_markers.hmm GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:55:20,232] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:55:20,241] [INFO] Found 6/6 markers.
[2023-06-13 02:55:20,296] [INFO] Query marker FASTA was written to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/markers.fasta
[2023-06-13 02:55:20,296] [INFO] Task started: Blastn
[2023-06-13 02:55:20,297] [INFO] Running command: blastn -query GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/reference_markers.fasta -out GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:55:20,972] [INFO] Task succeeded: Blastn
[2023-06-13 02:55:20,976] [INFO] Selected 26 target genomes.
[2023-06-13 02:55:20,976] [INFO] Target genome list was writen to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/target_genomes.txt
[2023-06-13 02:55:20,980] [INFO] Task started: fastANI
[2023-06-13 02:55:20,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg20013480-db8f-4a5f-8b31-0770bde58d78/GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna.gz --refList GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/target_genomes.txt --output GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:55:41,935] [INFO] Task succeeded: fastANI
[2023-06-13 02:55:41,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:55:41,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:55:41,951] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:55:41,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:55:41,952] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.4918	593	2207	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.2656	239	2207	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	75.1482	51	2207	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.1197	300	2207	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.1056	310	2207	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.03	315	2207	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	74.9998	67	2207	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	74.9986	72	2207	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	74.9752	80	2207	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	74.9454	74	2207	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	74.9425	74	2207	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	74.9328	63	2207	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	74.7881	67	2207	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	74.7432	68	2207	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:55:41,954] [INFO] DFAST Taxonomy check result was written to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/tc_result.tsv
[2023-06-13 02:55:41,954] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:55:41,955] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:55:41,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/checkm_data
[2023-06-13 02:55:41,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:55:42,023] [INFO] Task started: CheckM
[2023-06-13 02:55:42,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/checkm_input GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/checkm_result
[2023-06-13 02:56:36,996] [INFO] Task succeeded: CheckM
[2023-06-13 02:56:36,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:56:37,023] [INFO] ===== Completeness check finished =====
[2023-06-13 02:56:37,024] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:56:37,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/markers.fasta)
[2023-06-13 02:56:37,024] [INFO] Task started: Blastn
[2023-06-13 02:56:37,025] [INFO] Running command: blastn -query GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720e87e7-6987-4084-bbc6-7044ae0fc003/dqc_reference/reference_markers_gtdb.fasta -out GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:56:38,049] [INFO] Task succeeded: Blastn
[2023-06-13 02:56:38,054] [INFO] Selected 23 target genomes.
[2023-06-13 02:56:38,054] [INFO] Target genome list was writen to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:56:38,070] [INFO] Task started: fastANI
[2023-06-13 02:56:38,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg20013480-db8f-4a5f-8b31-0770bde58d78/GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna.gz --refList GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:56:56,331] [INFO] Task succeeded: fastANI
[2023-06-13 02:56:56,355] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:56:56,356] [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_017644045.1	s__UBA1660 sp017644045	76.4199	465	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.3138	467	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	76.2973	213	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	76.2327	357	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_009992505.1	s__JAADHO01 sp009992505	76.2033	176	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151775.1	s__JAADHO01 sp013151775	76.0524	214	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647035.1	s__SG8-38 sp003647035	75.821	75	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	-
GCA_017303575.1	s__JAFLCL01 sp017303575	75.7812	375	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303415.1	s__SG8-38 sp001303415	75.7709	72	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213565.1	s__MED-G138 sp004213565	75.7123	371	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__MED-G138	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002645.1	s__SG8-38 sp013002645	75.567	65	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881055.1	s__JADGRF01 sp017881055	75.535	152	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712745.1	s__JADJQN01 sp016712745	75.3447	92	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJQN01;g__JADJQN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212965.1	s__JACRDA01 sp016212965	74.767	268	2207	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	74.7369	86	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:56:56,358] [INFO] GTDB search result was written to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:56:56,359] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:56:56,362] [INFO] DFAST_QC result json was written to GCA_938024995.1_R4_Bin_MAXBIN_061_1_genomic.fna/dqc_result.json
[2023-06-13 02:56:56,362] [INFO] DFAST_QC completed!
[2023-06-13 02:56:56,362] [INFO] Total running time: 0h1m56s