[2023-07-01 02:42:37,649] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:42:37,652] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:42:37,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference
[2023-07-01 02:42:39,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:42:39,213] [INFO] Task started: Prodigal
[2023-07-01 02:42:39,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg465c1a23-1e46-48a0-ab09-355bab55144a/GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna.gz | prodigal -d GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/cds.fna -a GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:42:45,717] [INFO] Task succeeded: Prodigal
[2023-07-01 02:42:45,717] [INFO] Task started: HMMsearch
[2023-07-01 02:42:45,717] [INFO] Running command: hmmsearch --tblout GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/reference_markers.hmm GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:42:45,968] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:42:45,970] [INFO] Found 6/6 markers.
[2023-07-01 02:42:46,005] [INFO] Query marker FASTA was written to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/markers.fasta
[2023-07-01 02:42:46,006] [INFO] Task started: Blastn
[2023-07-01 02:42:46,006] [INFO] Running command: blastn -query GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/reference_markers.fasta -out GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:42:46,729] [INFO] Task succeeded: Blastn
[2023-07-01 02:42:46,736] [INFO] Selected 20 target genomes.
[2023-07-01 02:42:46,737] [INFO] Target genome list was writen to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/target_genomes.txt
[2023-07-01 02:42:46,738] [INFO] Task started: fastANI
[2023-07-01 02:42:46,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg465c1a23-1e46-48a0-ab09-355bab55144a/GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna.gz --refList GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/target_genomes.txt --output GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:43:00,950] [INFO] Task succeeded: fastANI
[2023-07-01 02:43:00,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:43:00,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:43:00,964] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:43:00,964] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:43:00,964] [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
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	81.402	417	616	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	80.6156	398	616	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	78.2644	246	616	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	78.142	255	616	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	77.7249	239	616	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	77.1423	146	616	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.4713	63	616	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	76.1898	55	616	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	76.1323	55	616	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.1048	61	616	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	75.984	57	616	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	75.9119	58	616	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	75.9021	58	616	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:43:00,966] [INFO] DFAST Taxonomy check result was written to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/tc_result.tsv
[2023-07-01 02:43:00,967] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:43:00,967] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:43:00,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/checkm_data
[2023-07-01 02:43:00,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:43:00,996] [INFO] Task started: CheckM
[2023-07-01 02:43:00,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/checkm_input GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/checkm_result
[2023-07-01 02:43:26,841] [INFO] Task succeeded: CheckM
[2023-07-01 02:43:26,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 02:43:26,866] [INFO] ===== Completeness check finished =====
[2023-07-01 02:43:26,866] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:43:26,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/markers.fasta)
[2023-07-01 02:43:26,867] [INFO] Task started: Blastn
[2023-07-01 02:43:26,867] [INFO] Running command: blastn -query GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef0692a-d787-4450-a8bc-23a1ceff4256/dqc_reference/reference_markers_gtdb.fasta -out GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:43:28,011] [INFO] Task succeeded: Blastn
[2023-07-01 02:43:28,016] [INFO] Selected 9 target genomes.
[2023-07-01 02:43:28,016] [INFO] Target genome list was writen to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:43:28,044] [INFO] Task started: fastANI
[2023-07-01 02:43:28,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg465c1a23-1e46-48a0-ab09-355bab55144a/GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna.gz --refList GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/target_genomes_gtdb.txt --output GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:43:32,223] [INFO] Task succeeded: fastANI
[2023-07-01 02:43:32,238] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:43:32,238] [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_903821685.1	s__Sphingorhabdus_B sp903821685	99.601	527	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.60	99.60	0.86	0.86	2	conclusive
GCA_002278855.1	s__Sphingorhabdus_B sp002278855	86.59	502	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.65	99.65	0.97	0.97	2	-
GCA_016462305.1	s__Sphingorhabdus_B sp016462305	81.9436	342	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.63	98.63	0.82	0.82	2	-
GCF_003933235.1	s__Sphingorhabdus_B wooponensis	81.402	417	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868245.1	s__Sphingorhabdus_B sp903868245	81.2385	353	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299895.1	s__Sphingorhabdus_B sp002299895	81.0399	410	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282385.1	s__Sphingorhabdus_B sp002282385	80.6605	403	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.98	99.95	0.99	0.98	4	-
GCF_014196595.1	s__Sphingorhabdus_B rigui	80.6156	398	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479765.1	s__Sphingorhabdus_B sp002479765	80.3704	391	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:43:32,240] [INFO] GTDB search result was written to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/result_gtdb.tsv
[2023-07-01 02:43:32,241] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:43:32,244] [INFO] DFAST_QC result json was written to GCA_903941245.1_freshwater_MAG_---_Loc090402-4m_bin-0578_genomic.fna/dqc_result.json
[2023-07-01 02:43:32,244] [INFO] DFAST_QC completed!
[2023-07-01 02:43:32,244] [INFO] Total running time: 0h0m55s