[2024-01-25 18:11:05,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference
[2024-01-25 18:11:06,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,745] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg82a38c57-42a7-423b-876c-318c8831d69f/GCF_025790165.1_ASM2579016v1_genomic.fna.gz | prodigal -d GCF_025790165.1_ASM2579016v1_genomic.fna/cds.fna -a GCF_025790165.1_ASM2579016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:19,655] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:19,655] [INFO] Task started: HMMsearch
[2024-01-25 18:11:19,655] [INFO] Running command: hmmsearch --tblout GCF_025790165.1_ASM2579016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/reference_markers.hmm GCF_025790165.1_ASM2579016v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:19,928] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:19,929] [INFO] Found 6/6 markers.
[2024-01-25 18:11:19,977] [INFO] Query marker FASTA was written to GCF_025790165.1_ASM2579016v1_genomic.fna/markers.fasta
[2024-01-25 18:11:19,977] [INFO] Task started: Blastn
[2024-01-25 18:11:19,977] [INFO] Running command: blastn -query GCF_025790165.1_ASM2579016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/reference_markers.fasta -out GCF_025790165.1_ASM2579016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:21,061] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:21,064] [INFO] Selected 29 target genomes.
[2024-01-25 18:11:21,064] [INFO] Target genome list was writen to GCF_025790165.1_ASM2579016v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:21,091] [INFO] Task started: fastANI
[2024-01-25 18:11:21,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a38c57-42a7-423b-876c-318c8831d69f/GCF_025790165.1_ASM2579016v1_genomic.fna.gz --refList GCF_025790165.1_ASM2579016v1_genomic.fna/target_genomes.txt --output GCF_025790165.1_ASM2579016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:44,320] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:44,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:44,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:44,337] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:44,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:44,337] [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
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	78.2452	409	1638	95	below_threshold
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	78.2126	509	1638	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	78.119	420	1638	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	78.0505	409	1638	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	78.0095	430	1638	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	77.9856	408	1638	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.9804	446	1638	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	77.9245	420	1638	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	77.8598	385	1638	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.7934	435	1638	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.7739	359	1638	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	77.7301	381	1638	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.7216	467	1638	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	77.651	420	1638	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	77.6327	477	1638	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	77.6079	367	1638	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	77.5726	382	1638	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	77.5292	457	1638	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	77.5217	324	1638	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.4957	376	1638	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	77.4782	465	1638	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	77.4663	414	1638	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	77.3903	431	1638	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	77.3723	388	1638	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.1972	388	1638	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	77.114	414	1638	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	77.008	461	1638	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	76.1004	313	1638	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	76.075	377	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:44,339] [INFO] DFAST Taxonomy check result was written to GCF_025790165.1_ASM2579016v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:44,340] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:44,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:44,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/checkm_data
[2024-01-25 18:11:44,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:44,387] [INFO] Task started: CheckM
[2024-01-25 18:11:44,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025790165.1_ASM2579016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025790165.1_ASM2579016v1_genomic.fna/checkm_input GCF_025790165.1_ASM2579016v1_genomic.fna/checkm_result
[2024-01-25 18:12:30,045] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:30,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,079] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:30,079] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:30,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025790165.1_ASM2579016v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:30,081] [INFO] Task started: Blastn
[2024-01-25 18:12:30,081] [INFO] Running command: blastn -query GCF_025790165.1_ASM2579016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9790754f-83a8-4635-b572-4439dd639016/dqc_reference/reference_markers_gtdb.fasta -out GCF_025790165.1_ASM2579016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:31,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:31,935] [INFO] Selected 30 target genomes.
[2024-01-25 18:12:31,936] [INFO] Target genome list was writen to GCF_025790165.1_ASM2579016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:31,954] [INFO] Task started: fastANI
[2024-01-25 18:12:31,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a38c57-42a7-423b-876c-318c8831d69f/GCF_025790165.1_ASM2579016v1_genomic.fna.gz --refList GCF_025790165.1_ASM2579016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025790165.1_ASM2579016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:55,964] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:55,982] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:55,982] [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_014873655.1	s__Aeromicrobium sp014873655	78.3791	410	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039565.1	s__Aeromicrobium terrae	78.238	409	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127285.1	s__Mumia sp014127285	78.2376	460	1638	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	78.2	512	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065605.1	s__Aeromicrobium chenweiae	78.1273	419	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004336805.1	s__Aeromicrobium sp004336805	78.0771	404	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994095.1	s__Mumia xiangluensis	78.0693	497	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_003586285.1	s__Aeromicrobium endophyticum	78.035	426	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698185.1	s__JACCVL01 sp013698185	78.0264	213	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCVL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695785.1	s__JACCZT01 sp013695785	78.0157	267	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379735.1	s__WHTB01 sp009379735	77.9791	392	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__WHTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	77.9661	434	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	77.9096	496	1638	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_002384855.1	s__UBA4001 sp002384855	77.8116	369	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011299595.1	s__Marmoricola_A sp011299595	77.7419	405	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620705.1	s__Nocardioides sp000620705	77.7165	423	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	77.7076	481	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001653335.1	s__Nocardioides dokdonensis	77.6331	364	1638	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	77.6125	426	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	77.5794	381	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	77.5396	442	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	77.5091	460	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004919105.1	s__Nocardioides sp004919105	77.4979	391	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744365.1	s__Marmoricola sp017744365	77.4922	429	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	77.4902	393	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	77.4668	413	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	77.3539	435	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_000721265.1	s__Streptomyces sp000721265	76.3383	297	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	76.17	322	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_014650895.1	s__Streptomyces omiyaensis	76.0796	376	1638	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:55,984] [INFO] GTDB search result was written to GCF_025790165.1_ASM2579016v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:55,985] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:55,989] [INFO] DFAST_QC result json was written to GCF_025790165.1_ASM2579016v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:55,989] [INFO] DFAST_QC completed!
[2024-01-25 18:12:55,989] [INFO] Total running time: 0h1m50s