[2023-06-05 07:15:49,005] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:15:49,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:15:49,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference
[2023-06-05 07:15:50,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:15:50,388] [INFO] Task started: Prodigal
[2023-06-05 07:15:50,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg5367ab3b-55b7-4257-b0f2-d12070410989/GCA_902805825.1_AVDCRST-MAG29_genomic.fna.gz | prodigal -d GCA_902805825.1_AVDCRST-MAG29_genomic.fna/cds.fna -a GCA_902805825.1_AVDCRST-MAG29_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:15:58,316] [INFO] Task succeeded: Prodigal
[2023-06-05 07:15:58,316] [INFO] Task started: HMMsearch
[2023-06-05 07:15:58,316] [INFO] Running command: hmmsearch --tblout GCA_902805825.1_AVDCRST-MAG29_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/reference_markers.hmm GCA_902805825.1_AVDCRST-MAG29_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:15:58,613] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:15:58,614] [INFO] Found 6/6 markers.
[2023-06-05 07:15:58,659] [INFO] Query marker FASTA was written to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/markers.fasta
[2023-06-05 07:15:58,660] [INFO] Task started: Blastn
[2023-06-05 07:15:58,660] [INFO] Running command: blastn -query GCA_902805825.1_AVDCRST-MAG29_genomic.fna/markers.fasta -db /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/reference_markers.fasta -out GCA_902805825.1_AVDCRST-MAG29_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:15:59,855] [INFO] Task succeeded: Blastn
[2023-06-05 07:15:59,859] [INFO] Selected 25 target genomes.
[2023-06-05 07:15:59,859] [INFO] Target genome list was writen to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/target_genomes.txt
[2023-06-05 07:15:59,865] [INFO] Task started: fastANI
[2023-06-05 07:15:59,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg5367ab3b-55b7-4257-b0f2-d12070410989/GCA_902805825.1_AVDCRST-MAG29_genomic.fna.gz --refList GCA_902805825.1_AVDCRST-MAG29_genomic.fna/target_genomes.txt --output GCA_902805825.1_AVDCRST-MAG29_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:18,885] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:18,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:18,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:18,908] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:18,909] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:16:18,909] [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
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.7445	321	789	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.6923	266	789	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	78.5535	289	789	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	78.5252	328	789	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	78.5117	308	789	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	78.3928	292	789	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	78.3443	316	789	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	78.3387	316	789	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	78.3348	266	789	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	78.3022	292	789	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	78.2929	275	789	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	78.2518	276	789	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.2253	264	789	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	78.1358	285	789	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	78.1099	240	789	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	78.0744	314	789	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	78.0559	228	789	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	78.0366	255	789	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	78.0032	277	789	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.9918	255	789	95	below_threshold
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	77.9149	252	789	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	77.5259	232	789	95	below_threshold
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	77.4006	232	789	95	below_threshold
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	77.1964	233	789	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	76.8905	228	789	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:16:18,913] [INFO] DFAST Taxonomy check result was written to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/tc_result.tsv
[2023-06-05 07:16:18,913] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:18,913] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:18,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/checkm_data
[2023-06-05 07:16:18,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:18,948] [INFO] Task started: CheckM
[2023-06-05 07:16:18,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902805825.1_AVDCRST-MAG29_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902805825.1_AVDCRST-MAG29_genomic.fna/checkm_input GCA_902805825.1_AVDCRST-MAG29_genomic.fna/checkm_result
[2023-06-05 07:16:47,337] [INFO] Task succeeded: CheckM
[2023-06-05 07:16:47,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:16:47,366] [INFO] ===== Completeness check finished =====
[2023-06-05 07:16:47,367] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:16:47,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902805825.1_AVDCRST-MAG29_genomic.fna/markers.fasta)
[2023-06-05 07:16:47,368] [INFO] Task started: Blastn
[2023-06-05 07:16:47,368] [INFO] Running command: blastn -query GCA_902805825.1_AVDCRST-MAG29_genomic.fna/markers.fasta -db /var/lib/cwl/stg89e8153a-f512-4000-b346-23a23889d333/dqc_reference/reference_markers_gtdb.fasta -out GCA_902805825.1_AVDCRST-MAG29_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:49,116] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:49,121] [INFO] Selected 25 target genomes.
[2023-06-05 07:16:49,121] [INFO] Target genome list was writen to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:16:49,381] [INFO] Task started: fastANI
[2023-06-05 07:16:49,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg5367ab3b-55b7-4257-b0f2-d12070410989/GCA_902805825.1_AVDCRST-MAG29_genomic.fna.gz --refList GCA_902805825.1_AVDCRST-MAG29_genomic.fna/target_genomes_gtdb.txt --output GCA_902805825.1_AVDCRST-MAG29_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:17:08,011] [INFO] Task succeeded: fastANI
[2023-06-05 07:17:08,034] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 07:17:08,034] [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
GCF_019039255.1	s__JABFXA01 sp019039255	78.7467	321	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698185.1	s__JACCVL01 sp013698185	78.7363	233	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCVL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	78.6617	268	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	78.582	287	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	78.5618	325	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379735.1	s__WHTB01 sp009379735	78.5608	251	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__WHTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	78.5572	282	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_003752505.1	s__Marmoricola aurantiacus	78.5117	308	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426045.1	s__Marmoricola sp000426045	78.3564	285	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	78.3401	289	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009823805.1	s__Nocardioides sp009823805	78.2869	276	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872795.1	s__Nocardioides sp017872795	78.2865	262	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701885.1	s__Nocardioides sp009701885	78.24	262	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	78.1428	285	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	78.1255	239	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	78.0855	313	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644415.1	s__Marmoricola endophyticus	78.083	261	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319165.1	s__Nocardioides acrostichi	78.0712	227	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994095.1	s__Mumia xiangluensis	78.0687	252	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017744365.1	s__Marmoricola sp017744365	77.9916	301	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127285.1	s__Mumia sp014127285	77.9743	228	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	99.73	99.46	0.99	0.98	3	-
GCF_002797495.1	s__Mumia flava	77.9705	248	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	77.5258	232	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900104745.1	s__Actinopolymorpha singaporensis	77.4133	231	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100695.1	s__Klenkia brasiliensis	77.1974	235	789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:17:08,036] [INFO] GTDB search result was written to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/result_gtdb.tsv
[2023-06-05 07:17:08,036] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:17:08,041] [INFO] DFAST_QC result json was written to GCA_902805825.1_AVDCRST-MAG29_genomic.fna/dqc_result.json
[2023-06-05 07:17:08,042] [INFO] DFAST_QC completed!
[2023-06-05 07:17:08,042] [INFO] Total running time: 0h1m19s