[2024-01-24 13:36:44,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference
[2024-01-24 13:36:46,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,039] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,040] [INFO] Running command: gunzip -c /var/lib/cwl/stga8a103e8-1c0d-48ea-9735-750e507c24db/GCF_014199315.1_ASM1419931v1_genomic.fna.gz | prodigal -d GCF_014199315.1_ASM1419931v1_genomic.fna/cds.fna -a GCF_014199315.1_ASM1419931v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:56,750] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:56,750] [INFO] Task started: HMMsearch
[2024-01-24 13:36:56,751] [INFO] Running command: hmmsearch --tblout GCF_014199315.1_ASM1419931v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/reference_markers.hmm GCF_014199315.1_ASM1419931v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:57,063] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:57,064] [INFO] Found 6/6 markers.
[2024-01-24 13:36:57,098] [INFO] Query marker FASTA was written to GCF_014199315.1_ASM1419931v1_genomic.fna/markers.fasta
[2024-01-24 13:36:57,099] [INFO] Task started: Blastn
[2024-01-24 13:36:57,099] [INFO] Running command: blastn -query GCF_014199315.1_ASM1419931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/reference_markers.fasta -out GCF_014199315.1_ASM1419931v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:58,038] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:58,041] [INFO] Selected 20 target genomes.
[2024-01-24 13:36:58,041] [INFO] Target genome list was writen to GCF_014199315.1_ASM1419931v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:58,051] [INFO] Task started: fastANI
[2024-01-24 13:36:58,051] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a103e8-1c0d-48ea-9735-750e507c24db/GCF_014199315.1_ASM1419931v1_genomic.fna.gz --refList GCF_014199315.1_ASM1419931v1_genomic.fna/target_genomes.txt --output GCF_014199315.1_ASM1419931v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:10,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:10,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:10,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:10,401] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:10,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:10,401] [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
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	100.0	1138	1141	95	conclusive
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	99.9968	1140	1141	95	conclusive
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	79.5081	498	1141	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.0075	325	1141	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.8451	337	1141	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.6466	358	1141	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.6282	246	1141	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.5803	396	1141	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.5684	351	1141	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.5378	272	1141	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.4815	329	1141	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.4731	336	1141	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.3341	285	1141	95	below_threshold
Altericroceibacterium spongiae	strain=HN-Y73	GCA_003610805.1	2320269	2320269	type	True	78.2714	283	1141	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.1776	279	1141	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.1645	269	1141	95	below_threshold
Altericroceibacterium indicum	strain=DSM 18604	GCA_009828105.1	374177	374177	type	True	78.1385	238	1141	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	77.9411	232	1141	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.7936	285	1141	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.7818	241	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:10,403] [INFO] DFAST Taxonomy check result was written to GCF_014199315.1_ASM1419931v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:10,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:10,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:10,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/checkm_data
[2024-01-24 13:37:10,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:10,449] [INFO] Task started: CheckM
[2024-01-24 13:37:10,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199315.1_ASM1419931v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199315.1_ASM1419931v1_genomic.fna/checkm_input GCF_014199315.1_ASM1419931v1_genomic.fna/checkm_result
[2024-01-24 13:37:47,767] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:47,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:47,789] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:47,789] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:47,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199315.1_ASM1419931v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:47,790] [INFO] Task started: Blastn
[2024-01-24 13:37:47,791] [INFO] Running command: blastn -query GCF_014199315.1_ASM1419931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e03e8e-897d-43a4-b9b1-28a4b4cc8940/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199315.1_ASM1419931v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:49,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:49,399] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:49,399] [INFO] Target genome list was writen to GCF_014199315.1_ASM1419931v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:49,423] [INFO] Task started: fastANI
[2024-01-24 13:37:49,424] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a103e8-1c0d-48ea-9735-750e507c24db/GCF_014199315.1_ASM1419931v1_genomic.fna.gz --refList GCF_014199315.1_ASM1419931v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199315.1_ASM1419931v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:00,824] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:00,845] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:00,846] [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_001008165.2	s__Croceibacterium atlanticum	99.9968	1140	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003569745.1	s__Croceibacterium sp003569745	80.9757	643	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.7649	266	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	79.735	476	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	79.4883	500	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.2369	469	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	79.0131	473	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.8114	420	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.7813	369	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	78.692	289	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.5905	405	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.5845	395	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.4881	329	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827595.1	s__Altericroceibacterium endophyticum	78.3525	344	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.3341	285	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	78.2206	318	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599195.1	s__Croceibacterium sp018599195	78.1837	329	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	77.8712	262	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,847] [INFO] GTDB search result was written to GCF_014199315.1_ASM1419931v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:00,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:00,852] [INFO] DFAST_QC result json was written to GCF_014199315.1_ASM1419931v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:00,852] [INFO] DFAST_QC completed!
[2024-01-24 13:38:00,852] [INFO] Total running time: 0h1m16s