[2024-01-25 19:01:20,850] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:20,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:20,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference
[2024-01-25 19:01:21,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:21,987] [INFO] Task started: Prodigal
[2024-01-25 19:01:21,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0275054-e88e-4a85-84df-fa1d91d2cfc1/GCF_014197795.1_ASM1419779v1_genomic.fna.gz | prodigal -d GCF_014197795.1_ASM1419779v1_genomic.fna/cds.fna -a GCF_014197795.1_ASM1419779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:32,572] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:32,572] [INFO] Task started: HMMsearch
[2024-01-25 19:01:32,572] [INFO] Running command: hmmsearch --tblout GCF_014197795.1_ASM1419779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/reference_markers.hmm GCF_014197795.1_ASM1419779v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:32,780] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:32,782] [INFO] Found 6/6 markers.
[2024-01-25 19:01:32,815] [INFO] Query marker FASTA was written to GCF_014197795.1_ASM1419779v1_genomic.fna/markers.fasta
[2024-01-25 19:01:32,816] [INFO] Task started: Blastn
[2024-01-25 19:01:32,816] [INFO] Running command: blastn -query GCF_014197795.1_ASM1419779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/reference_markers.fasta -out GCF_014197795.1_ASM1419779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:33,704] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:33,708] [INFO] Selected 13 target genomes.
[2024-01-25 19:01:33,708] [INFO] Target genome list was writen to GCF_014197795.1_ASM1419779v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:33,723] [INFO] Task started: fastANI
[2024-01-25 19:01:33,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0275054-e88e-4a85-84df-fa1d91d2cfc1/GCF_014197795.1_ASM1419779v1_genomic.fna.gz --refList GCF_014197795.1_ASM1419779v1_genomic.fna/target_genomes.txt --output GCF_014197795.1_ASM1419779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:47,257] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:47,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:47,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:47,266] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:47,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:47,266] [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
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	100.0	1356	1360	95	conclusive
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	81.9336	826	1360	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	80.6454	721	1360	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	80.6002	738	1360	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	80.5994	731	1360	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	77.3555	294	1360	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.3307	366	1360	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5843	186	1360	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.4589	395	1360	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.1917	312	1360	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.1769	316	1360	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.0092	243	1360	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.9856	391	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:47,270] [INFO] DFAST Taxonomy check result was written to GCF_014197795.1_ASM1419779v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:47,270] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:47,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:47,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/checkm_data
[2024-01-25 19:01:47,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:47,314] [INFO] Task started: CheckM
[2024-01-25 19:01:47,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197795.1_ASM1419779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197795.1_ASM1419779v1_genomic.fna/checkm_input GCF_014197795.1_ASM1419779v1_genomic.fna/checkm_result
[2024-01-25 19:02:27,164] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:27,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:27,188] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:27,189] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:27,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197795.1_ASM1419779v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:27,190] [INFO] Task started: Blastn
[2024-01-25 19:02:27,190] [INFO] Running command: blastn -query GCF_014197795.1_ASM1419779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0e4c07-d1e6-47f0-a0b0-18d77db53d5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197795.1_ASM1419779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:28,930] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:28,933] [INFO] Selected 7 target genomes.
[2024-01-25 19:02:28,933] [INFO] Target genome list was writen to GCF_014197795.1_ASM1419779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:28,957] [INFO] Task started: fastANI
[2024-01-25 19:02:28,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0275054-e88e-4a85-84df-fa1d91d2cfc1/GCF_014197795.1_ASM1419779v1_genomic.fna.gz --refList GCF_014197795.1_ASM1419779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197795.1_ASM1419779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:37,102] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:37,108] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:37,108] [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_014197795.1	s__Rhodospira goensis	100.0	1356	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009601025.1	s__Rhodospira navarrensis	81.9139	827	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	81.3945	731	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	80.8482	755	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	80.6156	727	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCF_014925385.1	s__WHTV01 sp014925385	77.3348	365	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	77.3265	297	1360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:37,109] [INFO] GTDB search result was written to GCF_014197795.1_ASM1419779v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:37,110] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:37,113] [INFO] DFAST_QC result json was written to GCF_014197795.1_ASM1419779v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:37,114] [INFO] DFAST_QC completed!
[2024-01-25 19:02:37,114] [INFO] Total running time: 0h1m16s