[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference
[2024-01-25 17:34:08,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,950] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg92301954-d930-4d41-96d6-165e42faedcd/GCF_013370205.1_ASM1337020v1_genomic.fna.gz | prodigal -d GCF_013370205.1_ASM1337020v1_genomic.fna/cds.fna -a GCF_013370205.1_ASM1337020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:16,594] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:16,594] [INFO] Task started: HMMsearch
[2024-01-25 17:34:16,594] [INFO] Running command: hmmsearch --tblout GCF_013370205.1_ASM1337020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/reference_markers.hmm GCF_013370205.1_ASM1337020v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:16,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:16,898] [INFO] Found 6/6 markers.
[2024-01-25 17:34:16,924] [INFO] Query marker FASTA was written to GCF_013370205.1_ASM1337020v1_genomic.fna/markers.fasta
[2024-01-25 17:34:16,924] [INFO] Task started: Blastn
[2024-01-25 17:34:16,925] [INFO] Running command: blastn -query GCF_013370205.1_ASM1337020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/reference_markers.fasta -out GCF_013370205.1_ASM1337020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:17,727] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:17,730] [INFO] Selected 28 target genomes.
[2024-01-25 17:34:17,731] [INFO] Target genome list was writen to GCF_013370205.1_ASM1337020v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:17,793] [INFO] Task started: fastANI
[2024-01-25 17:34:17,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg92301954-d930-4d41-96d6-165e42faedcd/GCF_013370205.1_ASM1337020v1_genomic.fna.gz --refList GCF_013370205.1_ASM1337020v1_genomic.fna/target_genomes.txt --output GCF_013370205.1_ASM1337020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:34,486] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:34,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:34,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:34,506] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:34,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:34,506] [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
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.4401	394	969	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.0427	310	969	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.9758	375	969	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.958	377	969	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.9451	388	969	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.9371	413	969	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.8625	376	969	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.8123	358	969	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.8028	412	969	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.6867	340	969	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.6864	321	969	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.5901	367	969	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.5876	368	969	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.5655	345	969	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.5356	307	969	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.5079	345	969	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	78.4742	261	969	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	78.4125	323	969	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.3383	354	969	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.2932	354	969	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.2319	340	969	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.2156	293	969	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.0073	239	969	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.8056	241	969	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.7787	273	969	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	77.7546	206	969	95	below_threshold
Alteripontixanthobacter maritimus	strain=HME9302	GCA_003340475.1	2161824	2161824	type	True	77.7384	246	969	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.7018	244	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:34,514] [INFO] DFAST Taxonomy check result was written to GCF_013370205.1_ASM1337020v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:34,515] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:34,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:34,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/checkm_data
[2024-01-25 17:34:34,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:34,552] [INFO] Task started: CheckM
[2024-01-25 17:34:34,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013370205.1_ASM1337020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013370205.1_ASM1337020v1_genomic.fna/checkm_input GCF_013370205.1_ASM1337020v1_genomic.fna/checkm_result
[2024-01-25 17:34:59,994] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:59,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:00,017] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:00,017] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:00,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013370205.1_ASM1337020v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:00,017] [INFO] Task started: Blastn
[2024-01-25 17:35:00,017] [INFO] Running command: blastn -query GCF_013370205.1_ASM1337020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4e536f-31bb-4aa2-a38e-9f3203275129/dqc_reference/reference_markers_gtdb.fasta -out GCF_013370205.1_ASM1337020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:01,378] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:01,381] [INFO] Selected 24 target genomes.
[2024-01-25 17:35:01,381] [INFO] Target genome list was writen to GCF_013370205.1_ASM1337020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:01,400] [INFO] Task started: fastANI
[2024-01-25 17:35:01,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg92301954-d930-4d41-96d6-165e42faedcd/GCF_013370205.1_ASM1337020v1_genomic.fna.gz --refList GCF_013370205.1_ASM1337020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013370205.1_ASM1337020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:17,294] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:17,308] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:17,308] [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_013370205.1	s__Actirhodobacter atriluteus	100.0	969	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827325.1	s__Qipengyuania vulgaris	81.2316	334	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827635.1	s__Parapontixanthobacter aurantiacus	80.1225	445	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parapontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.4242	376	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.415	396	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.9633	377	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.9455	387	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.6943	369	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.5991	367	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.5033	346	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	78.4739	366	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_003355455.1	s__Qipengyuania aurea	78.4283	318	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_003958625.1	s__Tsuneonella rigui	78.4121	323	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.3441	299	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	78.2568	280	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911865.1	s__Qipengyuania sp013911865	78.2452	237	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	78.2301	316	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCF_000331285.1	s__Erythrobacter sp000331285	78.1983	313	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	78.161	275	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	78.1492	314	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCA_017744735.1	s__Caenibius sp017744735	78.0663	288	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.8646	292	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	77.8156	240	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_013336795.1	s__Pseudopontixanthobacter muriae	77.812	273	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:17,309] [INFO] GTDB search result was written to GCF_013370205.1_ASM1337020v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:17,310] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:17,314] [INFO] DFAST_QC result json was written to GCF_013370205.1_ASM1337020v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:17,314] [INFO] DFAST_QC completed!
[2024-01-25 17:35:17,314] [INFO] Total running time: 0h1m10s