[2023-06-30 20:35:31,025] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:35:31,027] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:35:31,028] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference
[2023-06-30 20:35:33,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:35:33,702] [INFO] Task started: Prodigal
[2023-06-30 20:35:33,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg2844645a-38a1-495b-9f0b-2b06455c034d/GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna.gz | prodigal -d GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/cds.fna -a GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:35:42,068] [INFO] Task succeeded: Prodigal
[2023-06-30 20:35:42,068] [INFO] Task started: HMMsearch
[2023-06-30 20:35:42,069] [INFO] Running command: hmmsearch --tblout GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/reference_markers.hmm GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:35:42,347] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:35:42,349] [INFO] Found 6/6 markers.
[2023-06-30 20:35:42,382] [INFO] Query marker FASTA was written to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/markers.fasta
[2023-06-30 20:35:42,383] [INFO] Task started: Blastn
[2023-06-30 20:35:42,383] [INFO] Running command: blastn -query GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/reference_markers.fasta -out GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:35:43,180] [INFO] Task succeeded: Blastn
[2023-06-30 20:35:43,184] [INFO] Selected 23 target genomes.
[2023-06-30 20:35:43,184] [INFO] Target genome list was writen to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/target_genomes.txt
[2023-06-30 20:35:43,190] [INFO] Task started: fastANI
[2023-06-30 20:35:43,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg2844645a-38a1-495b-9f0b-2b06455c034d/GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna.gz --refList GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/target_genomes.txt --output GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:35:57,567] [INFO] Task succeeded: fastANI
[2023-06-30 20:35:57,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:35:57,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:35:57,590] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:35:57,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:35:57,591] [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
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	78.5407	358	885	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	77.9191	261	885	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.858	250	885	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	77.8399	232	885	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	77.8392	263	885	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	77.8273	259	885	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	77.7846	228	885	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	77.6292	214	885	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.54	263	885	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.5118	227	885	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	77.4642	208	885	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	77.4281	210	885	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	77.3768	219	885	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.349	204	885	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	77.3471	205	885	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	77.2678	210	885	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.2327	185	885	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.2098	231	885	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	76.9784	167	885	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	76.9219	154	885	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	76.9073	162	885	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	76.9028	136	885	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	75.8087	81	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:35:57,593] [INFO] DFAST Taxonomy check result was written to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/tc_result.tsv
[2023-06-30 20:35:57,594] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:35:57,594] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:35:57,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/checkm_data
[2023-06-30 20:35:57,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:35:57,630] [INFO] Task started: CheckM
[2023-06-30 20:35:57,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/checkm_input GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/checkm_result
[2023-06-30 20:36:27,290] [INFO] Task succeeded: CheckM
[2023-06-30 20:36:27,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.49%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:36:27,315] [INFO] ===== Completeness check finished =====
[2023-06-30 20:36:27,315] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:36:27,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/markers.fasta)
[2023-06-30 20:36:27,316] [INFO] Task started: Blastn
[2023-06-30 20:36:27,316] [INFO] Running command: blastn -query GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda5a6b1-877f-4aa0-83f2-0ecd0bb73d63/dqc_reference/reference_markers_gtdb.fasta -out GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:36:28,624] [INFO] Task succeeded: Blastn
[2023-06-30 20:36:28,629] [INFO] Selected 17 target genomes.
[2023-06-30 20:36:28,629] [INFO] Target genome list was writen to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:36:28,637] [INFO] Task started: fastANI
[2023-06-30 20:36:28,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg2844645a-38a1-495b-9f0b-2b06455c034d/GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna.gz --refList GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/target_genomes_gtdb.txt --output GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:36:41,325] [INFO] Task succeeded: fastANI
[2023-06-30 20:36:41,351] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:36:41,352] [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_903828145.1	s__Devosia_A sp903828145	99.9692	855	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.95	99.93	0.97	0.97	4	conclusive
GCA_001899085.1	s__Devosia_A sp001899085	78.6731	392	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_001425235.1	s__Devosia_A sp001425235	78.6611	375	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_001402915.1	s__Devosia_A sp001402915	78.5499	372	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970465.2	s__Devosia_A insulae	78.5419	358	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	78.5391	351	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCA_016713105.1	s__Devosia_A sp016713105	78.4702	367	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842455.1	s__Devosia_A sp903842455	78.3627	347	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144345.1	s__Devosia_A sp004144345	78.2736	274	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873135.1	s__Devosia_A sp014873135	78.2389	322	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899065.1	s__Devosia_A sp001899065	78.0193	273	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.96	98.00	0.93	0.88	3	-
GCF_900119845.1	s__Devosia_A enhydra	77.9056	262	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657675.1	s__Devosia_A sp015657675	77.8827	290	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056405.1	s__Devosia indica	77.5118	227	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004005995.1	s__Devosia sp004005995	77.407	219	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.21	97.18	0.88	0.88	3	-
GCF_009758415.1	s__Devosia marina	77.3897	218	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_000230555.1	s__Pelagibacterium halotolerans	76.9091	162	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-06-30 20:36:41,354] [INFO] GTDB search result was written to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/result_gtdb.tsv
[2023-06-30 20:36:41,354] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:36:41,359] [INFO] DFAST_QC result json was written to GCA_903939155.1_freshwater_MAG_---_Loc081215-8m_bin-0062_genomic.fna/dqc_result.json
[2023-06-30 20:36:41,359] [INFO] DFAST_QC completed!
[2023-06-30 20:36:41,359] [INFO] Total running time: 0h1m10s