[2023-06-17 14:48:35,382] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:35,387] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:35,388] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference
[2023-06-17 14:48:36,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:48:36,608] [INFO] Task started: Prodigal
[2023-06-17 14:48:36,608] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5256b51-9ac0-4c1e-a727-9dc262c417a0/GCA_028287005.1_ASM2828700v1_genomic.fna.gz | prodigal -d GCA_028287005.1_ASM2828700v1_genomic.fna/cds.fna -a GCA_028287005.1_ASM2828700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:48:54,359] [INFO] Task succeeded: Prodigal
[2023-06-17 14:48:54,359] [INFO] Task started: HMMsearch
[2023-06-17 14:48:54,359] [INFO] Running command: hmmsearch --tblout GCA_028287005.1_ASM2828700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/reference_markers.hmm GCA_028287005.1_ASM2828700v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:48:54,740] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:48:54,742] [INFO] Found 6/6 markers.
[2023-06-17 14:48:54,801] [INFO] Query marker FASTA was written to GCA_028287005.1_ASM2828700v1_genomic.fna/markers.fasta
[2023-06-17 14:48:54,801] [INFO] Task started: Blastn
[2023-06-17 14:48:54,801] [INFO] Running command: blastn -query GCA_028287005.1_ASM2828700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/reference_markers.fasta -out GCA_028287005.1_ASM2828700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:48:55,525] [INFO] Task succeeded: Blastn
[2023-06-17 14:48:55,530] [INFO] Selected 34 target genomes.
[2023-06-17 14:48:55,530] [INFO] Target genome list was writen to GCA_028287005.1_ASM2828700v1_genomic.fna/target_genomes.txt
[2023-06-17 14:48:55,533] [INFO] Task started: fastANI
[2023-06-17 14:48:55,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5256b51-9ac0-4c1e-a727-9dc262c417a0/GCA_028287005.1_ASM2828700v1_genomic.fna.gz --refList GCA_028287005.1_ASM2828700v1_genomic.fna/target_genomes.txt --output GCA_028287005.1_ASM2828700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:49:22,313] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:22,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:49:22,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:49:22,337] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:49:22,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:49:22,337] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3033	402	1831	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	75.0748	65	1831	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.0316	177	1831	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	74.9961	86	1831	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	74.9634	109	1831	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	74.9514	112	1831	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.9478	252	1831	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	74.8871	120	1831	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8849	227	1831	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	74.8751	66	1831	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8699	138	1831	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	74.8682	69	1831	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	74.8548	67	1831	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.8524	203	1831	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.8379	73	1831	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	74.8327	86	1831	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.8305	115	1831	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.8268	119	1831	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	74.8116	59	1831	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	74.809	56	1831	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	74.8073	119	1831	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.7892	78	1831	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	74.7721	112	1831	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	74.7506	95	1831	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	74.7422	60	1831	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	74.6926	72	1831	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	74.6396	91	1831	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:49:22,340] [INFO] DFAST Taxonomy check result was written to GCA_028287005.1_ASM2828700v1_genomic.fna/tc_result.tsv
[2023-06-17 14:49:22,340] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:49:22,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:49:22,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/checkm_data
[2023-06-17 14:49:22,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:49:22,415] [INFO] Task started: CheckM
[2023-06-17 14:49:22,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028287005.1_ASM2828700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028287005.1_ASM2828700v1_genomic.fna/checkm_input GCA_028287005.1_ASM2828700v1_genomic.fna/checkm_result
[2023-06-17 14:50:15,382] [INFO] Task succeeded: CheckM
[2023-06-17 14:50:15,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.80%
Contamintation: 8.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 14:50:15,413] [INFO] ===== Completeness check finished =====
[2023-06-17 14:50:15,414] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:50:15,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028287005.1_ASM2828700v1_genomic.fna/markers.fasta)
[2023-06-17 14:50:15,415] [INFO] Task started: Blastn
[2023-06-17 14:50:15,415] [INFO] Running command: blastn -query GCA_028287005.1_ASM2828700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2208574-af34-4015-b9c8-10a03d052598/dqc_reference/reference_markers_gtdb.fasta -out GCA_028287005.1_ASM2828700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:50:16,558] [INFO] Task succeeded: Blastn
[2023-06-17 14:50:16,564] [INFO] Selected 27 target genomes.
[2023-06-17 14:50:16,564] [INFO] Target genome list was writen to GCA_028287005.1_ASM2828700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:50:16,580] [INFO] Task started: fastANI
[2023-06-17 14:50:16,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5256b51-9ac0-4c1e-a727-9dc262c417a0/GCA_028287005.1_ASM2828700v1_genomic.fna.gz --refList GCA_028287005.1_ASM2828700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028287005.1_ASM2828700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:50:44,854] [INFO] Task succeeded: fastANI
[2023-06-17 14:50:44,879] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:50:44,880] [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_017881055.1	s__JADGRF01 sp017881055	75.8418	179	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009992505.1	s__JAADHO01 sp009992505	75.6315	91	1831	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_017881185.1	s__JADGRF01 sp017881185	75.5212	163	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	75.5105	138	1831	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_016706685.1	s__JADJJE01 sp016706685	75.4381	211	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCF_000737325.1	s__Sandaracinus amylolyticus	75.3136	397	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.255	144	1831	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_017644045.1	s__UBA1660 sp017644045	75.2248	180	1831	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_017303575.1	s__JAFLCL01 sp017303575	75.2105	248	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828805.1	s__Sandaracinus sp903828805	75.1722	134	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151775.1	s__JAADHO01 sp013151775	75.1523	142	1831	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_002699025.1	s__GCA-2699025 sp002699025	75.0814	234	1831	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_016712745.1	s__JADJQN01 sp016712745	75.0376	59	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJQN01;g__JADJQN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	75.0244	288	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298625.1	s__Ga0077539 sp013298625	74.9701	234	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__Ga0077539	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	74.9213	277	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	74.8991	123	1831	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022145.1	s__Anaeromyxobacter dehalogenans	74.8768	136	1831	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	-
GCA_016212965.1	s__JACRDA01 sp016212965	74.8743	220	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144585.1	s__Polyangium fumosum	74.8583	197	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	74.8571	132	1831	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297655.1	s__JAAFHV01 sp013297655	74.8373	145	1831	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	74.8033	72	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:50:44,882] [INFO] GTDB search result was written to GCA_028287005.1_ASM2828700v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:50:44,882] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:50:44,887] [INFO] DFAST_QC result json was written to GCA_028287005.1_ASM2828700v1_genomic.fna/dqc_result.json
[2023-06-17 14:50:44,888] [INFO] DFAST_QC completed!
[2023-06-17 14:50:44,888] [INFO] Total running time: 0h2m10s