[2023-06-30 05:18:16,988] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:18:16,990] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:18:16,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference
[2023-06-30 05:18:19,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:18:19,124] [INFO] Task started: Prodigal
[2023-06-30 05:18:19,125] [INFO] Running command: gunzip -c /var/lib/cwl/stg00913a5c-dd13-403c-9b32-a2712de4e647/GCA_024226735.1_ASM2422673v1_genomic.fna.gz | prodigal -d GCA_024226735.1_ASM2422673v1_genomic.fna/cds.fna -a GCA_024226735.1_ASM2422673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:18:42,360] [INFO] Task succeeded: Prodigal
[2023-06-30 05:18:42,361] [INFO] Task started: HMMsearch
[2023-06-30 05:18:42,362] [INFO] Running command: hmmsearch --tblout GCA_024226735.1_ASM2422673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/reference_markers.hmm GCA_024226735.1_ASM2422673v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:18:42,755] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:18:42,762] [INFO] Found 6/6 markers.
[2023-06-30 05:18:42,834] [INFO] Query marker FASTA was written to GCA_024226735.1_ASM2422673v1_genomic.fna/markers.fasta
[2023-06-30 05:18:42,835] [INFO] Task started: Blastn
[2023-06-30 05:18:42,835] [INFO] Running command: blastn -query GCA_024226735.1_ASM2422673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/reference_markers.fasta -out GCA_024226735.1_ASM2422673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:18:43,481] [INFO] Task succeeded: Blastn
[2023-06-30 05:18:43,487] [INFO] Selected 31 target genomes.
[2023-06-30 05:18:43,488] [INFO] Target genome list was writen to GCA_024226735.1_ASM2422673v1_genomic.fna/target_genomes.txt
[2023-06-30 05:18:43,519] [INFO] Task started: fastANI
[2023-06-30 05:18:43,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg00913a5c-dd13-403c-9b32-a2712de4e647/GCA_024226735.1_ASM2422673v1_genomic.fna.gz --refList GCA_024226735.1_ASM2422673v1_genomic.fna/target_genomes.txt --output GCA_024226735.1_ASM2422673v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:19:08,480] [INFO] Task succeeded: fastANI
[2023-06-30 05:19:08,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:19:08,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:19:08,506] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:19:08,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:19:08,506] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.081	58	2711	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.9213	144	2711	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	74.8814	66	2711	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.8735	241	2711	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	74.862	94	2711	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	74.8518	210	2711	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	74.8427	202	2711	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	74.8411	83	2711	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	74.8248	171	2711	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.8076	231	2711	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	74.8061	144	2711	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8032	228	2711	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.7966	218	2711	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	74.7949	70	2711	95	below_threshold
Burkholderia territorii	strain=LMG 28158	GCA_902833055.1	1503055	1503055	type	True	74.7934	236	2711	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	74.7866	142	2711	95	below_threshold
Burkholderia vietnamiensis	strain=FDAARGOS_1488	GCA_020099355.1	60552	60552	type	True	74.7848	284	2711	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_000959445.1	60552	60552	type	True	74.7842	284	2711	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_902830295.1	60552	60552	type	True	74.7822	285	2711	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.774	261	2711	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	74.7719	350	2711	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	74.7647	259	2711	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	74.758	208	2711	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.7577	147	2711	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	74.7562	194	2711	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	74.7552	196	2711	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	74.6879	106	2711	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	74.6691	149	2711	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	74.6547	67	2711	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	74.643	146	2711	95	below_threshold
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	74.6356	70	2711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:19:08,510] [INFO] DFAST Taxonomy check result was written to GCA_024226735.1_ASM2422673v1_genomic.fna/tc_result.tsv
[2023-06-30 05:19:08,510] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:19:08,510] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:19:08,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/checkm_data
[2023-06-30 05:19:08,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:19:08,602] [INFO] Task started: CheckM
[2023-06-30 05:19:08,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024226735.1_ASM2422673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024226735.1_ASM2422673v1_genomic.fna/checkm_input GCA_024226735.1_ASM2422673v1_genomic.fna/checkm_result
[2023-06-30 05:20:19,322] [INFO] Task succeeded: CheckM
[2023-06-30 05:20:19,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:20:19,347] [INFO] ===== Completeness check finished =====
[2023-06-30 05:20:19,348] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:20:19,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024226735.1_ASM2422673v1_genomic.fna/markers.fasta)
[2023-06-30 05:20:19,348] [INFO] Task started: Blastn
[2023-06-30 05:20:19,349] [INFO] Running command: blastn -query GCA_024226735.1_ASM2422673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9765c06b-1277-422c-84f7-2cd60ff70f05/dqc_reference/reference_markers_gtdb.fasta -out GCA_024226735.1_ASM2422673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:20:20,295] [INFO] Task succeeded: Blastn
[2023-06-30 05:20:20,299] [INFO] Selected 23 target genomes.
[2023-06-30 05:20:20,299] [INFO] Target genome list was writen to GCA_024226735.1_ASM2422673v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:20:20,310] [INFO] Task started: fastANI
[2023-06-30 05:20:20,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg00913a5c-dd13-403c-9b32-a2712de4e647/GCA_024226735.1_ASM2422673v1_genomic.fna.gz --refList GCA_024226735.1_ASM2422673v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024226735.1_ASM2422673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:20:38,296] [INFO] Task succeeded: fastANI
[2023-06-30 05:20:38,318] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:20:38,319] [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_002720975.1	s__GCA-2720975 sp002720975	77.0843	139	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	96.24	96.24	0.74	0.74	2	-
GCA_011524785.1	s__GCA-2686945 sp011524785	76.8448	262	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	76.8263	434	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779225.1	s__GCA-2686945 sp016779225	76.7563	256	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	76.6606	362	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686265.1	s__GCA-2686265 sp002686265	76.6542	345	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872715.1	s__F1-120-MAGs118 sp016872715	76.6009	383	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.5511	320	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	76.5317	375	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	76.5115	320	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	76.5059	433	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	76.5046	254	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	76.3945	255	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	76.2502	429	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	76.2486	394	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.1163	382	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	76.1126	268	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.0977	418	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	76.0573	391	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.0445	389	2711	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331285.1	s__Erythrobacter sp000331285	75.1001	67	2711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	74.9381	61	2711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253705.1	s__Humitalea rosea	74.6532	94	2711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Humitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:20:38,321] [INFO] GTDB search result was written to GCA_024226735.1_ASM2422673v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:20:38,321] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:20:38,327] [INFO] DFAST_QC result json was written to GCA_024226735.1_ASM2422673v1_genomic.fna/dqc_result.json
[2023-06-30 05:20:38,327] [INFO] DFAST_QC completed!
[2023-06-30 05:20:38,327] [INFO] Total running time: 0h2m21s