[2023-06-16 21:17:29,374] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:17:29,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:17:29,376] [INFO] DQC Reference Directory: /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference
[2023-06-16 21:17:30,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:17:30,610] [INFO] Task started: Prodigal
[2023-06-16 21:17:30,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a3876ce-5555-4c41-8743-928a388e6a5a/GCA_009692135.1_ASM969213v1_genomic.fna.gz | prodigal -d GCA_009692135.1_ASM969213v1_genomic.fna/cds.fna -a GCA_009692135.1_ASM969213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:17:36,181] [INFO] Task succeeded: Prodigal
[2023-06-16 21:17:36,182] [INFO] Task started: HMMsearch
[2023-06-16 21:17:36,182] [INFO] Running command: hmmsearch --tblout GCA_009692135.1_ASM969213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/reference_markers.hmm GCA_009692135.1_ASM969213v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:17:36,437] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:17:36,438] [INFO] Found 6/6 markers.
[2023-06-16 21:17:36,465] [INFO] Query marker FASTA was written to GCA_009692135.1_ASM969213v1_genomic.fna/markers.fasta
[2023-06-16 21:17:36,465] [INFO] Task started: Blastn
[2023-06-16 21:17:36,465] [INFO] Running command: blastn -query GCA_009692135.1_ASM969213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/reference_markers.fasta -out GCA_009692135.1_ASM969213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:17:37,299] [INFO] Task succeeded: Blastn
[2023-06-16 21:17:37,303] [INFO] Selected 32 target genomes.
[2023-06-16 21:17:37,303] [INFO] Target genome list was writen to GCA_009692135.1_ASM969213v1_genomic.fna/target_genomes.txt
[2023-06-16 21:17:37,309] [INFO] Task started: fastANI
[2023-06-16 21:17:37,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3876ce-5555-4c41-8743-928a388e6a5a/GCA_009692135.1_ASM969213v1_genomic.fna.gz --refList GCA_009692135.1_ASM969213v1_genomic.fna/target_genomes.txt --output GCA_009692135.1_ASM969213v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:18:03,630] [INFO] Task succeeded: fastANI
[2023-06-16 21:18:03,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:18:03,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:18:03,647] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:18:03,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 21:18:03,647] [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
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.6922	101	684	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.6699	103	684	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.6369	106	684	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.6047	190	684	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	75.0576	69	684	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.9566	111	684	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.9528	111	684	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	74.945	88	684	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	74.9299	97	684	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.9134	102	684	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	74.9131	61	684	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	74.9038	98	684	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	74.8767	98	684	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.8752	123	684	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	74.8554	114	684	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.8346	81	684	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	74.8042	83	684	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.7871	127	684	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	74.778	53	684	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.7671	61	684	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	74.757	63	684	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:18:03,650] [INFO] DFAST Taxonomy check result was written to GCA_009692135.1_ASM969213v1_genomic.fna/tc_result.tsv
[2023-06-16 21:18:03,650] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:18:03,650] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:18:03,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/checkm_data
[2023-06-16 21:18:03,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:18:03,683] [INFO] Task started: CheckM
[2023-06-16 21:18:03,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009692135.1_ASM969213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009692135.1_ASM969213v1_genomic.fna/checkm_input GCA_009692135.1_ASM969213v1_genomic.fna/checkm_result
[2023-06-16 21:18:26,515] [INFO] Task succeeded: CheckM
[2023-06-16 21:18:26,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:18:26,539] [INFO] ===== Completeness check finished =====
[2023-06-16 21:18:26,540] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:18:26,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009692135.1_ASM969213v1_genomic.fna/markers.fasta)
[2023-06-16 21:18:26,541] [INFO] Task started: Blastn
[2023-06-16 21:18:26,541] [INFO] Running command: blastn -query GCA_009692135.1_ASM969213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc659e428-9ad6-4d9f-aec3-90b08ac4e7a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_009692135.1_ASM969213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:18:27,797] [INFO] Task succeeded: Blastn
[2023-06-16 21:18:27,801] [INFO] Selected 24 target genomes.
[2023-06-16 21:18:27,801] [INFO] Target genome list was writen to GCA_009692135.1_ASM969213v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:18:27,836] [INFO] Task started: fastANI
[2023-06-16 21:18:27,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3876ce-5555-4c41-8743-928a388e6a5a/GCA_009692135.1_ASM969213v1_genomic.fna.gz --refList GCA_009692135.1_ASM969213v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009692135.1_ASM969213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:18:43,735] [INFO] Task succeeded: fastANI
[2023-06-16 21:18:43,750] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 21:18:43,751] [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_009692205.1	s__UBA2982 sp009692205	80.9267	156	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	77.1668	171	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126575.1	s__SLBA01 sp007126575	76.7919	77	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.74	99.74	0.94	0.94	2	-
GCA_009838975.1	s__Bin94 sp009838975	76.6365	83	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.37	98.63	0.95	0.92	5	-
GCA_018678395.1	s__IDS-52 sp018678395	76.5143	107	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__IDS-52	95.0	98.28	98.28	0.76	0.76	2	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.4032	118	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121455.1	s__SKKN01 sp007121455	76.3155	65	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKKN01	95.0	99.94	99.94	0.95	0.95	3	-
GCA_009841475.1	s__Bin94 sp009841475	76.2459	97	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.08	98.52	0.89	0.85	6	-
GCA_007692665.1	s__SKNW01 sp007692665	76.2087	76	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242735.1	s__RSA9 sp003242735	76.1456	120	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__RSA9	95.0	99.82	99.82	0.92	0.92	2	-
GCA_012267435.1	s__BD2-11 sp012267435	76.1183	54	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840215.1	s__Bin94 sp009840215	75.9658	81	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.38	99.00	0.93	0.91	6	-
GCA_015664885.1	s__UBA1138 sp003447875	75.9485	77	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_011362545.1	s__DSTP01 sp011362545	75.9335	114	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820915.1	s__JACDHR01 sp013820915	75.7764	57	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__JACDHR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221005.1	s__AG25 sp003221005	75.681	70	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG25	95.0	99.09	99.09	0.79	0.79	2	-
GCF_014202995.1	s__Longimicrobium terrae	75.6673	103	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__Longimicrobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_007130605.1	s__SLBA01 sp007130605	75.6014	54	684	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.40	99.31	0.83	0.83	4	-
GCA_016713535.1	s__JADJOY01 sp016713535	74.8717	118	684	d__Bacteria;p__JADJOY01;c__JADJOY01;o__JADJOY01;f__JADJOY01;g__JADJOY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:18:43,752] [INFO] GTDB search result was written to GCA_009692135.1_ASM969213v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:18:43,753] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:18:43,757] [INFO] DFAST_QC result json was written to GCA_009692135.1_ASM969213v1_genomic.fna/dqc_result.json
[2023-06-16 21:18:43,757] [INFO] DFAST_QC completed!
[2023-06-16 21:18:43,757] [INFO] Total running time: 0h1m14s