[2024-01-24 11:52:04,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference
[2024-01-24 11:52:05,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,896] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c8ac9a4-7823-40c0-a99d-9221600ee7ae/GCF_900445155.1_52067_E01_genomic.fna.gz | prodigal -d GCF_900445155.1_52067_E01_genomic.fna/cds.fna -a GCF_900445155.1_52067_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:18,829] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:18,830] [INFO] Task started: HMMsearch
[2024-01-24 11:52:18,830] [INFO] Running command: hmmsearch --tblout GCF_900445155.1_52067_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/reference_markers.hmm GCF_900445155.1_52067_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:19,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:19,100] [INFO] Found 6/6 markers.
[2024-01-24 11:52:19,144] [INFO] Query marker FASTA was written to GCF_900445155.1_52067_E01_genomic.fna/markers.fasta
[2024-01-24 11:52:19,144] [INFO] Task started: Blastn
[2024-01-24 11:52:19,144] [INFO] Running command: blastn -query GCF_900445155.1_52067_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/reference_markers.fasta -out GCF_900445155.1_52067_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:20,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:20,033] [INFO] Selected 22 target genomes.
[2024-01-24 11:52:20,033] [INFO] Target genome list was writen to GCF_900445155.1_52067_E01_genomic.fna/target_genomes.txt
[2024-01-24 11:52:20,042] [INFO] Task started: fastANI
[2024-01-24 11:52:20,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8ac9a4-7823-40c0-a99d-9221600ee7ae/GCF_900445155.1_52067_E01_genomic.fna.gz --refList GCF_900445155.1_52067_E01_genomic.fna/target_genomes.txt --output GCF_900445155.1_52067_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:41,937] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:41,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:41,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:41,958] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:41,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:41,958] [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
Afipia felis	strain=NCTC12499	GCA_900445155.1	1035	1035	type	True	100.0	1397	1397	95	conclusive
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	99.9962	1392	1397	95	conclusive
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	83.6385	886	1397	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	83.6225	884	1397	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	80.112	570	1397	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	80.0178	585	1397	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	79.9922	582	1397	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	79.9774	571	1397	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.8667	596	1397	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.7412	529	1397	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.6739	554	1397	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.6625	542	1397	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.5958	519	1397	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	79.4772	537	1397	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	79.4662	584	1397	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	79.4366	559	1397	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	79.3866	510	1397	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	79.2982	510	1397	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	77.8375	281	1397	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	77.36	205	1397	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	76.494	92	1397	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	76.3298	90	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,960] [INFO] DFAST Taxonomy check result was written to GCF_900445155.1_52067_E01_genomic.fna/tc_result.tsv
[2024-01-24 11:52:41,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:41,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:41,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/checkm_data
[2024-01-24 11:52:41,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:42,005] [INFO] Task started: CheckM
[2024-01-24 11:52:42,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445155.1_52067_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445155.1_52067_E01_genomic.fna/checkm_input GCF_900445155.1_52067_E01_genomic.fna/checkm_result
[2024-01-24 11:53:22,559] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:22,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:22,581] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:22,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:22,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445155.1_52067_E01_genomic.fna/markers.fasta)
[2024-01-24 11:53:22,582] [INFO] Task started: Blastn
[2024-01-24 11:53:22,582] [INFO] Running command: blastn -query GCF_900445155.1_52067_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgaea53cf1-a783-4428-9ee4-4b4bc19e3e37/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445155.1_52067_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:24,162] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:24,166] [INFO] Selected 17 target genomes.
[2024-01-24 11:53:24,167] [INFO] Target genome list was writen to GCF_900445155.1_52067_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:24,180] [INFO] Task started: fastANI
[2024-01-24 11:53:24,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8ac9a4-7823-40c0-a99d-9221600ee7ae/GCF_900445155.1_52067_E01_genomic.fna.gz --refList GCF_900445155.1_52067_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445155.1_52067_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:43,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:43,246] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:43,246] [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_000314735.2	s__Afipia felis	99.9962	1392	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.60	95.79	0.96	0.87	4	conclusive
GCF_000178995.1	s__Afipia sp000178995	88.3612	1044	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.46	98.22	0.89	0.84	3	-
GCF_000218565.1	s__Afipia carboxidovorans	83.6313	887	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.99	99.99	1.00	1.00	3	-
GCA_001897755.1	s__Afipia sp001897755	81.6518	697	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017305455.1	s__Afipia sp017305455	81.5483	654	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308575.1	s__Afipia sp001897905	80.4159	609	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001425835.1	s__Afipia sp001425835	80.4078	623	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963145.1	s__Afipia sp003963145	80.1365	598	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314675.2	s__Afipia broomeae	80.0326	583	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCF_008932115.1	s__Bradyrhizobium betae	79.9608	588	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	79.6657	591	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCA_017474385.1	s__Afipia sp017474385	79.6189	450	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215605.1	s__Rhodopseudomonas palustris_L	79.5523	543	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	79.4131	550	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129685.1	s__Bradyrhizobium manausense_D	79.3669	533	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114605.1	s__Tardiphaga sp900114605	78.9359	472	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	98.23	98.23	0.94	0.94	2	-
GCA_017308135.1	s__Tagaea sp017308135	77.33	140	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	97.31	97.31	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:43,248] [INFO] GTDB search result was written to GCF_900445155.1_52067_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:43,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:43,253] [INFO] DFAST_QC result json was written to GCF_900445155.1_52067_E01_genomic.fna/dqc_result.json
[2024-01-24 11:53:43,254] [INFO] DFAST_QC completed!
[2024-01-24 11:53:43,254] [INFO] Total running time: 0h1m39s