[2023-06-30 03:33:02,585] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:33:02,587] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:33:02,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference
[2023-06-30 03:33:04,016] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:33:04,017] [INFO] Task started: Prodigal
[2023-06-30 03:33:04,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg7699a110-dd33-48b4-8f60-0a9ce40f7d25/GCA_024236115.1_ASM2423611v1_genomic.fna.gz | prodigal -d GCA_024236115.1_ASM2423611v1_genomic.fna/cds.fna -a GCA_024236115.1_ASM2423611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:33:11,549] [INFO] Task succeeded: Prodigal
[2023-06-30 03:33:11,550] [INFO] Task started: HMMsearch
[2023-06-30 03:33:11,550] [INFO] Running command: hmmsearch --tblout GCA_024236115.1_ASM2423611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/reference_markers.hmm GCA_024236115.1_ASM2423611v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:33:11,811] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:33:11,812] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7699a110-dd33-48b4-8f60-0a9ce40f7d25/GCA_024236115.1_ASM2423611v1_genomic.fna.gz]
[2023-06-30 03:33:11,835] [INFO] Query marker FASTA was written to GCA_024236115.1_ASM2423611v1_genomic.fna/markers.fasta
[2023-06-30 03:33:11,835] [INFO] Task started: Blastn
[2023-06-30 03:33:11,835] [INFO] Running command: blastn -query GCA_024236115.1_ASM2423611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/reference_markers.fasta -out GCA_024236115.1_ASM2423611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:12,945] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:12,950] [INFO] Selected 20 target genomes.
[2023-06-30 03:33:12,950] [INFO] Target genome list was writen to GCA_024236115.1_ASM2423611v1_genomic.fna/target_genomes.txt
[2023-06-30 03:33:12,956] [INFO] Task started: fastANI
[2023-06-30 03:33:12,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg7699a110-dd33-48b4-8f60-0a9ce40f7d25/GCA_024236115.1_ASM2423611v1_genomic.fna.gz --refList GCA_024236115.1_ASM2423611v1_genomic.fna/target_genomes.txt --output GCA_024236115.1_ASM2423611v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:24,045] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:24,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:24,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:24,061] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:24,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:33:24,062] [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
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.9859	350	762	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.8902	332	762	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.8317	310	762	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.7127	340	762	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5568	319	762	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.5133	322	762	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.4572	303	762	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.4426	342	762	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.4119	326	762	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.3565	305	762	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.3513	302	762	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.2891	319	762	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.2863	305	762	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.26	309	762	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.2366	308	762	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.2236	321	762	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.9488	299	762	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.9165	317	762	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.5971	261	762	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.2154	246	762	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:33:24,064] [INFO] DFAST Taxonomy check result was written to GCA_024236115.1_ASM2423611v1_genomic.fna/tc_result.tsv
[2023-06-30 03:33:24,065] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:24,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:24,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/checkm_data
[2023-06-30 03:33:24,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:24,095] [INFO] Task started: CheckM
[2023-06-30 03:33:24,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024236115.1_ASM2423611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024236115.1_ASM2423611v1_genomic.fna/checkm_input GCA_024236115.1_ASM2423611v1_genomic.fna/checkm_result
[2023-06-30 03:33:52,295] [INFO] Task succeeded: CheckM
[2023-06-30 03:33:52,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:33:52,315] [INFO] ===== Completeness check finished =====
[2023-06-30 03:33:52,315] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:33:52,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024236115.1_ASM2423611v1_genomic.fna/markers.fasta)
[2023-06-30 03:33:52,316] [INFO] Task started: Blastn
[2023-06-30 03:33:52,316] [INFO] Running command: blastn -query GCA_024236115.1_ASM2423611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba7f14a-8602-4e16-b82f-e6de314161ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_024236115.1_ASM2423611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:53,843] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:53,849] [INFO] Selected 19 target genomes.
[2023-06-30 03:33:53,849] [INFO] Target genome list was writen to GCA_024236115.1_ASM2423611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:33:53,862] [INFO] Task started: fastANI
[2023-06-30 03:33:53,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg7699a110-dd33-48b4-8f60-0a9ce40f7d25/GCA_024236115.1_ASM2423611v1_genomic.fna.gz --refList GCA_024236115.1_ASM2423611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024236115.1_ASM2423611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:34:04,739] [INFO] Task succeeded: fastANI
[2023-06-30 03:34:04,759] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:34:04,760] [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_004114695.1	s__Parerythrobacter sp004114695	81.0098	430	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	80.4859	435	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.9802	348	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001542855.1	s__Qipengyuania sp001542855	79.8027	348	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	79.6004	341	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	79.5914	319	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.589	317	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	79.5452	319	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	79.4778	330	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.4367	342	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	79.3217	331	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.2737	320	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.2231	318	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.1802	297	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461955.1	s__QFOP01 sp003248785	79.1347	251	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__QFOP01	95.0	98.23	98.19	0.91	0.89	3	-
GCF_001635685.1	s__Qipengyuania sp001635685	79.1267	310	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	79.088	159	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	78.9979	305	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018819685.1	s__Qipengyuania sp018819685	78.6947	201	762	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:34:04,762] [INFO] GTDB search result was written to GCA_024236115.1_ASM2423611v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:34:04,763] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:34:04,768] [INFO] DFAST_QC result json was written to GCA_024236115.1_ASM2423611v1_genomic.fna/dqc_result.json
[2023-06-30 03:34:04,768] [INFO] DFAST_QC completed!
[2023-06-30 03:34:04,768] [INFO] Total running time: 0h1m2s