[2023-06-30 11:37:52,906] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:37:52,908] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:37:52,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference
[2023-06-30 11:37:54,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:37:54,143] [INFO] Task started: Prodigal
[2023-06-30 11:37:54,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg38fa068e-e57e-4ba1-adec-e667e824ed59/GCA_025936035.1_ASM2593603v1_genomic.fna.gz | prodigal -d GCA_025936035.1_ASM2593603v1_genomic.fna/cds.fna -a GCA_025936035.1_ASM2593603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:38:08,344] [INFO] Task succeeded: Prodigal
[2023-06-30 11:38:08,344] [INFO] Task started: HMMsearch
[2023-06-30 11:38:08,345] [INFO] Running command: hmmsearch --tblout GCA_025936035.1_ASM2593603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/reference_markers.hmm GCA_025936035.1_ASM2593603v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:38:08,635] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:38:08,636] [INFO] Found 6/6 markers.
[2023-06-30 11:38:08,678] [INFO] Query marker FASTA was written to GCA_025936035.1_ASM2593603v1_genomic.fna/markers.fasta
[2023-06-30 11:38:08,679] [INFO] Task started: Blastn
[2023-06-30 11:38:08,679] [INFO] Running command: blastn -query GCA_025936035.1_ASM2593603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/reference_markers.fasta -out GCA_025936035.1_ASM2593603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:38:09,352] [INFO] Task succeeded: Blastn
[2023-06-30 11:38:09,356] [INFO] Selected 23 target genomes.
[2023-06-30 11:38:09,356] [INFO] Target genome list was writen to GCA_025936035.1_ASM2593603v1_genomic.fna/target_genomes.txt
[2023-06-30 11:38:09,359] [INFO] Task started: fastANI
[2023-06-30 11:38:09,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fa068e-e57e-4ba1-adec-e667e824ed59/GCA_025936035.1_ASM2593603v1_genomic.fna.gz --refList GCA_025936035.1_ASM2593603v1_genomic.fna/target_genomes.txt --output GCA_025936035.1_ASM2593603v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:38:29,298] [INFO] Task succeeded: fastANI
[2023-06-30 11:38:29,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:38:29,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:38:29,317] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:38:29,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 11:38:29,318] [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	76.337	395	1613	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	75.938	134	1613	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	75.6474	77	1613	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	75.5978	56	1613	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4024	65	1613	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.6934	89	1613	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	74.632	118	1613	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	74.6306	78	1613	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	74.6085	93	1613	95	below_threshold
Acrocarpospora corrugata	strain=NBRC 13972	GCA_009687845.1	35763	35763	type	True	74.6072	66	1613	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.6025	52	1613	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	74.5707	100	1613	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	74.5611	57	1613	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:38:29,320] [INFO] DFAST Taxonomy check result was written to GCA_025936035.1_ASM2593603v1_genomic.fna/tc_result.tsv
[2023-06-30 11:38:29,320] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:38:29,320] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:38:29,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/checkm_data
[2023-06-30 11:38:29,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:38:29,370] [INFO] Task started: CheckM
[2023-06-30 11:38:29,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025936035.1_ASM2593603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025936035.1_ASM2593603v1_genomic.fna/checkm_input GCA_025936035.1_ASM2593603v1_genomic.fna/checkm_result
[2023-06-30 11:39:13,075] [INFO] Task succeeded: CheckM
[2023-06-30 11:39:13,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:39:13,101] [INFO] ===== Completeness check finished =====
[2023-06-30 11:39:13,101] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:39:13,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025936035.1_ASM2593603v1_genomic.fna/markers.fasta)
[2023-06-30 11:39:13,102] [INFO] Task started: Blastn
[2023-06-30 11:39:13,102] [INFO] Running command: blastn -query GCA_025936035.1_ASM2593603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf96442a8-23a8-4a1d-ac8e-11f1170764d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_025936035.1_ASM2593603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:39:14,121] [INFO] Task succeeded: Blastn
[2023-06-30 11:39:14,126] [INFO] Selected 17 target genomes.
[2023-06-30 11:39:14,127] [INFO] Target genome list was writen to GCA_025936035.1_ASM2593603v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:39:14,134] [INFO] Task started: fastANI
[2023-06-30 11:39:14,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fa068e-e57e-4ba1-adec-e667e824ed59/GCA_025936035.1_ASM2593603v1_genomic.fna.gz --refList GCA_025936035.1_ASM2593603v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025936035.1_ASM2593603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:39:23,960] [INFO] Task succeeded: fastANI
[2023-06-30 11:39:23,981] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 11:39:23,981] [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_013361935.1	s__JABFXC01 sp013361935	76.92	249	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCA_013361335.1	s__AG11 sp013361335	76.775	268	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_013361745.1	s__JABFXC01 sp013361745	76.5841	157	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223455.1	s__AG11 sp003223455	76.5781	280	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820975.1	s__JACDHQ01 sp013820975	76.516	108	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACDHQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881585.1	s__Fen-1231 sp017881585	76.43	169	1613	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_002215645.1	s__AG11 sp002215645	76.4256	218	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813605.1	s__UBA4720 sp013813605	76.3643	74	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__UBA4720	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000522985.1	s__Gemmatirosa kalamazoonesis	76.3557	390	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194585.1	s__Fen-1231 sp016194585	76.3066	237	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_003171215.1	s__Fen-1231 sp003171215	76.2354	190	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	97.59	95.49	0.88	0.84	3	-
GCA_013697785.1	s__FEN-1250 sp013697785	76.2326	160	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__FEN-1250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378185.1	s__AG11 sp014378185	76.1238	116	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221805.1	s__UBA4720 sp003221805	76.115	92	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__UBA4720	95.0	98.78	98.78	0.86	0.86	2	-
GCA_003131365.1	s__UBA4720 sp003131365	75.6871	78	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__UBA4720	95.0	95.35	95.29	0.77	0.75	4	-
GCA_003221825.1	s__20CM-2-65-7 sp003221825	75.6663	60	1613	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-2-65-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:39:23,983] [INFO] GTDB search result was written to GCA_025936035.1_ASM2593603v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:39:23,984] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:39:23,988] [INFO] DFAST_QC result json was written to GCA_025936035.1_ASM2593603v1_genomic.fna/dqc_result.json
[2023-06-30 11:39:23,988] [INFO] DFAST_QC completed!
[2023-06-30 11:39:23,988] [INFO] Total running time: 0h1m31s