[2024-01-24 11:19:53,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference
[2024-01-24 11:19:55,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,155] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,155] [INFO] Running command: gunzip -c /var/lib/cwl/stgbff171ad-4db0-4cea-ae67-18e32d724fd0/GCF_021568905.1_ASM2156890v1_genomic.fna.gz | prodigal -d GCF_021568905.1_ASM2156890v1_genomic.fna/cds.fna -a GCF_021568905.1_ASM2156890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:06,137] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:06,137] [INFO] Task started: HMMsearch
[2024-01-24 11:20:06,137] [INFO] Running command: hmmsearch --tblout GCF_021568905.1_ASM2156890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/reference_markers.hmm GCF_021568905.1_ASM2156890v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:06,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:06,421] [INFO] Found 6/6 markers.
[2024-01-24 11:20:06,455] [INFO] Query marker FASTA was written to GCF_021568905.1_ASM2156890v1_genomic.fna/markers.fasta
[2024-01-24 11:20:06,455] [INFO] Task started: Blastn
[2024-01-24 11:20:06,455] [INFO] Running command: blastn -query GCF_021568905.1_ASM2156890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/reference_markers.fasta -out GCF_021568905.1_ASM2156890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:07,399] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:07,403] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:07,403] [INFO] Target genome list was writen to GCF_021568905.1_ASM2156890v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:07,412] [INFO] Task started: fastANI
[2024-01-24 11:20:07,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff171ad-4db0-4cea-ae67-18e32d724fd0/GCF_021568905.1_ASM2156890v1_genomic.fna.gz --refList GCF_021568905.1_ASM2156890v1_genomic.fna/target_genomes.txt --output GCF_021568905.1_ASM2156890v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:26,663] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:26,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:26,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:26,686] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:26,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:26,686] [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
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	83.7401	918	1311	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	83.6765	928	1311	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	83.0967	917	1311	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.0901	295	1311	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.0296	292	1311	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.9833	378	1311	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.9794	210	1311	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.8755	398	1311	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.8342	344	1311	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.8316	275	1311	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.7314	265	1311	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.5511	179	1311	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.5511	179	1311	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.5392	197	1311	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.4519	259	1311	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	76.4054	159	1311	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3423	287	1311	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	76.338	310	1311	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	76.336	326	1311	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.1644	267	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:26,688] [INFO] DFAST Taxonomy check result was written to GCF_021568905.1_ASM2156890v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:26,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:26,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:26,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/checkm_data
[2024-01-24 11:20:26,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:26,729] [INFO] Task started: CheckM
[2024-01-24 11:20:26,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021568905.1_ASM2156890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021568905.1_ASM2156890v1_genomic.fna/checkm_input GCF_021568905.1_ASM2156890v1_genomic.fna/checkm_result
[2024-01-24 11:21:05,973] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:05,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,998] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:05,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:05,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021568905.1_ASM2156890v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:05,999] [INFO] Task started: Blastn
[2024-01-24 11:21:05,999] [INFO] Running command: blastn -query GCF_021568905.1_ASM2156890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00d499f7-229a-4bd3-993c-90cdc0da4a70/dqc_reference/reference_markers_gtdb.fasta -out GCF_021568905.1_ASM2156890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:07,799] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:07,803] [INFO] Selected 18 target genomes.
[2024-01-24 11:21:07,803] [INFO] Target genome list was writen to GCF_021568905.1_ASM2156890v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:07,827] [INFO] Task started: fastANI
[2024-01-24 11:21:07,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff171ad-4db0-4cea-ae67-18e32d724fd0/GCF_021568905.1_ASM2156890v1_genomic.fna.gz --refList GCF_021568905.1_ASM2156890v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021568905.1_ASM2156890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:27,550] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:27,565] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:27,566] [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_003173055.1	s__Zavarzinia compransoris	83.7018	927	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003173035.1	s__Zavarzinia aquatilis	83.1	917	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590945.1	s__Zavarzinia sp003590945	81.0081	844	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	77.159	261	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.9789	359	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	76.9447	394	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.9263	278	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_003130795.1	s__Azospirillum thermophilum	76.8826	396	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.8067	277	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_003336875.1	s__Oleisolibacter albus	76.7698	268	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.6484	383	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000496075.1	s__Lutibaculum baratangense	76.5479	196	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131225.1	s__U87765 sp018131225	76.5479	272	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__U87765	95.0	100.00	100.00	1.00	1.00	5	-
GCF_016653355.1	s__Rhodoplanes elegans	76.4448	301	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_001653715.1	s__Methylobacterium platani	76.3499	325	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCA_009377375.1	s__WHUE01 sp009377375	76.3017	232	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	76.2643	182	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.2323	211	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:27,568] [INFO] GTDB search result was written to GCF_021568905.1_ASM2156890v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:27,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:27,573] [INFO] DFAST_QC result json was written to GCF_021568905.1_ASM2156890v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:27,574] [INFO] DFAST_QC completed!
[2024-01-24 11:21:27,574] [INFO] Total running time: 0h1m34s