[2024-01-25 19:43:50,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference
[2024-01-25 19:43:51,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,791] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg679fa583-e595-4801-a647-88399235e717/GCF_031454065.1_ASM3145406v1_genomic.fna.gz | prodigal -d GCF_031454065.1_ASM3145406v1_genomic.fna/cds.fna -a GCF_031454065.1_ASM3145406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:00,634] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:00,634] [INFO] Task started: HMMsearch
[2024-01-25 19:44:00,634] [INFO] Running command: hmmsearch --tblout GCF_031454065.1_ASM3145406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/reference_markers.hmm GCF_031454065.1_ASM3145406v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:00,862] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:00,863] [INFO] Found 6/6 markers.
[2024-01-25 19:44:00,895] [INFO] Query marker FASTA was written to GCF_031454065.1_ASM3145406v1_genomic.fna/markers.fasta
[2024-01-25 19:44:00,895] [INFO] Task started: Blastn
[2024-01-25 19:44:00,895] [INFO] Running command: blastn -query GCF_031454065.1_ASM3145406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/reference_markers.fasta -out GCF_031454065.1_ASM3145406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:01,871] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:01,874] [INFO] Selected 27 target genomes.
[2024-01-25 19:44:01,874] [INFO] Target genome list was writen to GCF_031454065.1_ASM3145406v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:01,889] [INFO] Task started: fastANI
[2024-01-25 19:44:01,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg679fa583-e595-4801-a647-88399235e717/GCF_031454065.1_ASM3145406v1_genomic.fna.gz --refList GCF_031454065.1_ASM3145406v1_genomic.fna/target_genomes.txt --output GCF_031454065.1_ASM3145406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:25,916] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:25,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:25,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:25,932] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:44:25,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:44:25,932] [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
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	80.7785	642	1234	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.6418	442	1234	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	78.5797	471	1234	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	78.5002	318	1234	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	78.4522	319	1234	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.4459	511	1234	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	78.3987	472	1234	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	78.3964	324	1234	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	78.3456	328	1234	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	78.3043	461	1234	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.2359	447	1234	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	78.2003	317	1234	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1637	401	1234	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	78.1513	426	1234	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	78.1449	409	1234	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	78.1015	393	1234	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.9907	363	1234	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.8697	349	1234	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	77.8684	446	1234	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.8393	400	1234	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	77.7899	473	1234	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	77.7157	402	1234	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	77.7124	490	1234	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.6857	510	1234	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.6855	494	1234	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.6765	310	1234	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	77.1712	357	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:25,933] [INFO] DFAST Taxonomy check result was written to GCF_031454065.1_ASM3145406v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:25,934] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:25,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:25,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/checkm_data
[2024-01-25 19:44:25,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:25,974] [INFO] Task started: CheckM
[2024-01-25 19:44:25,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454065.1_ASM3145406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454065.1_ASM3145406v1_genomic.fna/checkm_input GCF_031454065.1_ASM3145406v1_genomic.fna/checkm_result
[2024-01-25 19:44:58,474] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:58,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:58,492] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:58,492] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:58,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454065.1_ASM3145406v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:58,493] [INFO] Task started: Blastn
[2024-01-25 19:44:58,493] [INFO] Running command: blastn -query GCF_031454065.1_ASM3145406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec88484-df1d-48b2-b0dc-6f719de74ff2/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454065.1_ASM3145406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:00,308] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:00,311] [INFO] Selected 11 target genomes.
[2024-01-25 19:45:00,311] [INFO] Target genome list was writen to GCF_031454065.1_ASM3145406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:00,325] [INFO] Task started: fastANI
[2024-01-25 19:45:00,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg679fa583-e595-4801-a647-88399235e717/GCF_031454065.1_ASM3145406v1_genomic.fna.gz --refList GCF_031454065.1_ASM3145406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454065.1_ASM3145406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:10,177] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:10,184] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:10,184] [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_016907975.1	s__Methylopila capsulata	82.8384	787	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	82.5284	789	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	82.0526	764	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	81.3782	736	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	80.9372	660	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	80.7924	708	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	80.7717	643	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310425.1	s__Hansschlegelia quercus	80.3465	621	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	77.5237	376	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565775.1	s__SKGQ01 sp003565775	75.7556	57	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SKGQ01	95.0	99.57	99.57	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:10,188] [INFO] GTDB search result was written to GCF_031454065.1_ASM3145406v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:10,188] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:10,194] [INFO] DFAST_QC result json was written to GCF_031454065.1_ASM3145406v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:10,194] [INFO] DFAST_QC completed!
[2024-01-25 19:45:10,194] [INFO] Total running time: 0h1m20s