[2024-01-25 19:58:35,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:35,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:35,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference
[2024-01-25 19:58:36,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:36,574] [INFO] Task started: Prodigal
[2024-01-25 19:58:36,574] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7c39589-513a-494c-b721-86f2b5455419/GCF_014643535.1_ASM1464353v1_genomic.fna.gz | prodigal -d GCF_014643535.1_ASM1464353v1_genomic.fna/cds.fna -a GCF_014643535.1_ASM1464353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:56,889] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:56,889] [INFO] Task started: HMMsearch
[2024-01-25 19:58:56,889] [INFO] Running command: hmmsearch --tblout GCF_014643535.1_ASM1464353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/reference_markers.hmm GCF_014643535.1_ASM1464353v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:57,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:57,288] [INFO] Found 6/6 markers.
[2024-01-25 19:58:57,345] [INFO] Query marker FASTA was written to GCF_014643535.1_ASM1464353v1_genomic.fna/markers.fasta
[2024-01-25 19:58:57,345] [INFO] Task started: Blastn
[2024-01-25 19:58:57,345] [INFO] Running command: blastn -query GCF_014643535.1_ASM1464353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/reference_markers.fasta -out GCF_014643535.1_ASM1464353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:58,300] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:58,305] [INFO] Selected 25 target genomes.
[2024-01-25 19:58:58,305] [INFO] Target genome list was writen to GCF_014643535.1_ASM1464353v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:58,317] [INFO] Task started: fastANI
[2024-01-25 19:58:58,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c39589-513a-494c-b721-86f2b5455419/GCF_014643535.1_ASM1464353v1_genomic.fna.gz --refList GCF_014643535.1_ASM1464353v1_genomic.fna/target_genomes.txt --output GCF_014643535.1_ASM1464353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:25,593] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:25,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:25,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:25,607] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:25,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:25,608] [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
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	100.0	2419	2421	95	conclusive
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	77.3485	403	2421	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.3438	506	2421	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	77.2788	469	2421	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	77.1416	447	2421	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.1126	537	2421	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.079	524	2421	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.0772	533	2421	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.0498	528	2421	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9875	374	2421	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.977	428	2421	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.9713	657	2421	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.9443	643	2421	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.8442	464	2421	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.7781	241	2421	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5768	584	2421	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.5046	243	2421	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.4553	312	2421	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.2874	309	2421	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.1773	520	2421	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.1296	489	2421	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1287	213	2421	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.1185	213	2421	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1113	333	2421	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.0948	379	2421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:25,613] [INFO] DFAST Taxonomy check result was written to GCF_014643535.1_ASM1464353v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:25,613] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:25,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:25,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/checkm_data
[2024-01-25 19:59:25,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:25,681] [INFO] Task started: CheckM
[2024-01-25 19:59:25,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643535.1_ASM1464353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643535.1_ASM1464353v1_genomic.fna/checkm_input GCF_014643535.1_ASM1464353v1_genomic.fna/checkm_result
[2024-01-25 20:00:28,587] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:28,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:28,603] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:28,603] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:28,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643535.1_ASM1464353v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:28,604] [INFO] Task started: Blastn
[2024-01-25 20:00:28,605] [INFO] Running command: blastn -query GCF_014643535.1_ASM1464353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43853100-756a-49a8-b3ea-beae178be1c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643535.1_ASM1464353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:30,538] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:30,541] [INFO] Selected 25 target genomes.
[2024-01-25 20:00:30,541] [INFO] Target genome list was writen to GCF_014643535.1_ASM1464353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:30,562] [INFO] Task started: fastANI
[2024-01-25 20:00:30,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c39589-513a-494c-b721-86f2b5455419/GCF_014643535.1_ASM1464353v1_genomic.fna.gz --refList GCF_014643535.1_ASM1464353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643535.1_ASM1464353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:57,969] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:57,984] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:57,984] [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_014643535.1	s__Aliidongia dinghuensis	100.0	2419	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000518365.1	s__URHD0088 sp000518365	77.593	605	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	77.351	549	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897565.1	s__CAIXXC01 sp903897565	77.2799	299	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIXXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	77.1428	515	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	77.1373	493	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_014197805.1	s__Rhodospirillum_A centenum	77.1366	347	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130795.1	s__Azospirillum thermophilum	77.0823	522	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	77.0712	550	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000283655.1	s__Azospirillum lipoferum_C	77.0666	523	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	77.0555	536	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	77.0508	528	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	77.0149	701	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.9798	537	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364795.1	s__Azospirillum oryzae	76.9608	488	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_003116095.1	s__Azospirillum sp003116095	76.9481	559	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	76.9419	268	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	76.924	340	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.8761	279	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.6974	411	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.6894	344	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.5801	325	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941105.1	s__CAJANL01 sp903941105	76.5509	279	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903923205.1	s__CAIXXC01 sp903923205	76.5405	171	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIXXC01	95.0	99.31	99.28	0.80	0.76	3	-
GCA_005884825.1	s__AP-15 sp005884825	76.3997	172	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:57,986] [INFO] GTDB search result was written to GCF_014643535.1_ASM1464353v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:57,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:57,990] [INFO] DFAST_QC result json was written to GCF_014643535.1_ASM1464353v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:57,990] [INFO] DFAST_QC completed!
[2024-01-25 20:00:57,991] [INFO] Total running time: 0h2m23s