[2024-01-24 12:25:20,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference
[2024-01-24 12:25:22,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:22,013] [INFO] Task started: Prodigal
[2024-01-24 12:25:22,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg34eff392-2117-4d61-8c76-18988ee84449/GCF_001558155.1_ASM155815v1_genomic.fna.gz | prodigal -d GCF_001558155.1_ASM155815v1_genomic.fna/cds.fna -a GCF_001558155.1_ASM155815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:38,109] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:38,109] [INFO] Task started: HMMsearch
[2024-01-24 12:25:38,110] [INFO] Running command: hmmsearch --tblout GCF_001558155.1_ASM155815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/reference_markers.hmm GCF_001558155.1_ASM155815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:38,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:38,391] [INFO] Found 6/6 markers.
[2024-01-24 12:25:38,439] [INFO] Query marker FASTA was written to GCF_001558155.1_ASM155815v1_genomic.fna/markers.fasta
[2024-01-24 12:25:38,440] [INFO] Task started: Blastn
[2024-01-24 12:25:38,440] [INFO] Running command: blastn -query GCF_001558155.1_ASM155815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/reference_markers.fasta -out GCF_001558155.1_ASM155815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:39,341] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:39,346] [INFO] Selected 22 target genomes.
[2024-01-24 12:25:39,347] [INFO] Target genome list was writen to GCF_001558155.1_ASM155815v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:39,355] [INFO] Task started: fastANI
[2024-01-24 12:25:39,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg34eff392-2117-4d61-8c76-18988ee84449/GCF_001558155.1_ASM155815v1_genomic.fna.gz --refList GCF_001558155.1_ASM155815v1_genomic.fna/target_genomes.txt --output GCF_001558155.1_ASM155815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:57,407] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:57,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:57,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:57,430] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:25:57,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:57,430] [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
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	100.0	1713	1719	95	conclusive
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	91.2805	1389	1719	95	below_threshold
Aliiruegeria haliotis	strain=DSM 29328	GCA_003003255.1	1280846	1280846	type	True	79.7131	662	1719	95	below_threshold
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	79.1693	554	1719	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.246	399	1719	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2337	391	1719	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.1839	453	1719	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.1227	459	1719	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.0805	425	1719	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	78.0526	379	1719	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.9864	397	1719	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.9534	324	1719	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.9059	367	1719	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.7784	308	1719	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.6631	381	1719	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.647	353	1719	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.6287	376	1719	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.6255	367	1719	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.529	294	1719	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.5102	340	1719	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.3355	265	1719	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.3238	289	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:57,432] [INFO] DFAST Taxonomy check result was written to GCF_001558155.1_ASM155815v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:57,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:57,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:57,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/checkm_data
[2024-01-24 12:25:57,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:57,488] [INFO] Task started: CheckM
[2024-01-24 12:25:57,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001558155.1_ASM155815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001558155.1_ASM155815v1_genomic.fna/checkm_input GCF_001558155.1_ASM155815v1_genomic.fna/checkm_result
[2024-01-24 12:26:45,834] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:45,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:45,860] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:45,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:45,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001558155.1_ASM155815v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:45,861] [INFO] Task started: Blastn
[2024-01-24 12:26:45,862] [INFO] Running command: blastn -query GCF_001558155.1_ASM155815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d989e02-80e6-4e91-921a-2cd4e7efbc66/dqc_reference/reference_markers_gtdb.fasta -out GCF_001558155.1_ASM155815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:47,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:47,518] [INFO] Selected 13 target genomes.
[2024-01-24 12:26:47,518] [INFO] Target genome list was writen to GCF_001558155.1_ASM155815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:47,531] [INFO] Task started: fastANI
[2024-01-24 12:26:47,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg34eff392-2117-4d61-8c76-18988ee84449/GCF_001558155.1_ASM155815v1_genomic.fna.gz --refList GCF_001558155.1_ASM155815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001558155.1_ASM155815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:27:00,535] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:00,552] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:27:00,552] [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_001558155.1	s__Tropicimonas sabulilitoris	100.0	1713	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_900099935.1	s__Tropicimonas lutimaris	91.2759	1390	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004146235.1	s__Tropicimonas sp004146235	80.6868	805	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	80.6369	815	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003255.1	s__Tropicimonas haliotis	79.6974	664	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112335.1	s__Tropicimonas isoalkanivorans	79.1766	554	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.8975	456	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390845.1	s__Tropicimonas sp003390845	78.4719	518	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.1547	489	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.1528	418	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.8194	399	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	77.6213	377	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	77.6109	387	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:27:00,554] [INFO] GTDB search result was written to GCF_001558155.1_ASM155815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:27:00,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:27:00,559] [INFO] DFAST_QC result json was written to GCF_001558155.1_ASM155815v1_genomic.fna/dqc_result.json
[2024-01-24 12:27:00,559] [INFO] DFAST_QC completed!
[2024-01-24 12:27:00,559] [INFO] Total running time: 0h1m40s