[2023-06-29 12:17:59,242] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:17:59,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:17:59,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference
[2023-06-29 12:18:00,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:18:00,678] [INFO] Task started: Prodigal
[2023-06-29 12:18:00,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg4200e7f1-1a31-4e21-8047-b4ab29bec9dd/GCA_021802745.1_ASM2180274v1_genomic.fna.gz | prodigal -d GCA_021802745.1_ASM2180274v1_genomic.fna/cds.fna -a GCA_021802745.1_ASM2180274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:18:10,177] [INFO] Task succeeded: Prodigal
[2023-06-29 12:18:10,177] [INFO] Task started: HMMsearch
[2023-06-29 12:18:10,177] [INFO] Running command: hmmsearch --tblout GCA_021802745.1_ASM2180274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/reference_markers.hmm GCA_021802745.1_ASM2180274v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:18:10,429] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:18:10,430] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4200e7f1-1a31-4e21-8047-b4ab29bec9dd/GCA_021802745.1_ASM2180274v1_genomic.fna.gz]
[2023-06-29 12:18:10,462] [INFO] Query marker FASTA was written to GCA_021802745.1_ASM2180274v1_genomic.fna/markers.fasta
[2023-06-29 12:18:10,463] [INFO] Task started: Blastn
[2023-06-29 12:18:10,463] [INFO] Running command: blastn -query GCA_021802745.1_ASM2180274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/reference_markers.fasta -out GCA_021802745.1_ASM2180274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:18:11,155] [INFO] Task succeeded: Blastn
[2023-06-29 12:18:11,158] [INFO] Selected 16 target genomes.
[2023-06-29 12:18:11,159] [INFO] Target genome list was writen to GCA_021802745.1_ASM2180274v1_genomic.fna/target_genomes.txt
[2023-06-29 12:18:11,163] [INFO] Task started: fastANI
[2023-06-29 12:18:11,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg4200e7f1-1a31-4e21-8047-b4ab29bec9dd/GCA_021802745.1_ASM2180274v1_genomic.fna.gz --refList GCA_021802745.1_ASM2180274v1_genomic.fna/target_genomes.txt --output GCA_021802745.1_ASM2180274v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:18:26,322] [INFO] Task succeeded: fastANI
[2023-06-29 12:18:26,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:18:26,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:18:26,337] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:18:26,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:18:26,337] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.6643	335	951	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.3253	105	951	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.31	84	951	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.1199	131	951	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.8988	126	951	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.8632	99	951	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	74.8505	86	951	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	74.7724	83	951	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	74.7688	90	951	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	74.7428	74	951	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	74.7033	128	951	95	below_threshold
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	74.6851	62	951	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:18:26,342] [INFO] DFAST Taxonomy check result was written to GCA_021802745.1_ASM2180274v1_genomic.fna/tc_result.tsv
[2023-06-29 12:18:26,342] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:18:26,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:18:26,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/checkm_data
[2023-06-29 12:18:26,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:18:26,383] [INFO] Task started: CheckM
[2023-06-29 12:18:26,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021802745.1_ASM2180274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021802745.1_ASM2180274v1_genomic.fna/checkm_input GCA_021802745.1_ASM2180274v1_genomic.fna/checkm_result
[2023-06-29 12:19:00,413] [INFO] Task succeeded: CheckM
[2023-06-29 12:19:00,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:19:00,444] [INFO] ===== Completeness check finished =====
[2023-06-29 12:19:00,444] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:19:00,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021802745.1_ASM2180274v1_genomic.fna/markers.fasta)
[2023-06-29 12:19:00,445] [INFO] Task started: Blastn
[2023-06-29 12:19:00,446] [INFO] Running command: blastn -query GCA_021802745.1_ASM2180274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd0265c7-da79-43f7-8264-08602fc5de25/dqc_reference/reference_markers_gtdb.fasta -out GCA_021802745.1_ASM2180274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:19:01,512] [INFO] Task succeeded: Blastn
[2023-06-29 12:19:01,516] [INFO] Selected 13 target genomes.
[2023-06-29 12:19:01,516] [INFO] Target genome list was writen to GCA_021802745.1_ASM2180274v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:19:01,533] [INFO] Task started: fastANI
[2023-06-29 12:19:01,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg4200e7f1-1a31-4e21-8047-b4ab29bec9dd/GCA_021802745.1_ASM2180274v1_genomic.fna.gz --refList GCA_021802745.1_ASM2180274v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021802745.1_ASM2180274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:19:09,403] [INFO] Task succeeded: fastANI
[2023-06-29 12:19:09,421] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:19:09,421] [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_016218305.1	s__PNKL01 sp016218305	83.1854	412	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822425.1	s__PNKL01 sp013822425	82.8099	525	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182795.1	s__PNKL01 sp016182795	82.4763	550	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871855.1	s__PNKL01 sp016871855	81.96	476	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525845.1	s__PNKF01 sp011525845	77.9005	258	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	98.76	98.76	0.95	0.95	2	-
GCA_902825965.1	s__PNKF01 sp902825965	77.7369	250	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714015.1	s__PNKF01 sp016714015	77.7097	284	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874035.1	s__Fen-1231 sp016874035	77.312	141	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719105.1	s__SCN-70-22 sp016719105	77.1472	232	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	98.70	98.52	0.93	0.89	8	-
GCA_903906325.1	s__PNKF01 sp903906325	77.1202	115	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822285.1	s__PNKF01 sp013822285	77.0758	123	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002215645.1	s__AG11 sp002215645	76.6151	154	951	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:19:09,424] [INFO] GTDB search result was written to GCA_021802745.1_ASM2180274v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:19:09,425] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:19:09,430] [INFO] DFAST_QC result json was written to GCA_021802745.1_ASM2180274v1_genomic.fna/dqc_result.json
[2023-06-29 12:19:09,430] [INFO] DFAST_QC completed!
[2023-06-29 12:19:09,431] [INFO] Total running time: 0h1m10s