[2023-03-16 07:34:40,565] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,565] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference
[2023-03-16 07:34:42,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,228] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,228] [INFO] Running command: cat /var/lib/cwl/stg9d5fd4da-f283-4b87-ba80-eb751b0de132/OceanDNA-b31542.fa | prodigal -d OceanDNA-b31542/cds.fna -a OceanDNA-b31542/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:34:51,131] [INFO] Task succeeded: Prodigal
[2023-03-16 07:34:51,132] [INFO] Task started: HMMsearch
[2023-03-16 07:34:51,132] [INFO] Running command: hmmsearch --tblout OceanDNA-b31542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/reference_markers.hmm OceanDNA-b31542/protein.faa > /dev/null
[2023-03-16 07:34:51,263] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:34:51,263] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9d5fd4da-f283-4b87-ba80-eb751b0de132/OceanDNA-b31542.fa]
[2023-03-16 07:34:51,279] [INFO] Query marker FASTA was written to OceanDNA-b31542/markers.fasta
[2023-03-16 07:34:51,280] [INFO] Task started: Blastn
[2023-03-16 07:34:51,280] [INFO] Running command: blastn -query OceanDNA-b31542/markers.fasta -db /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/reference_markers.fasta -out OceanDNA-b31542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:34:51,826] [INFO] Task succeeded: Blastn
[2023-03-16 07:34:51,827] [INFO] Selected 12 target genomes.
[2023-03-16 07:34:51,827] [INFO] Target genome list was writen to OceanDNA-b31542/target_genomes.txt
[2023-03-16 07:34:51,896] [INFO] Task started: fastANI
[2023-03-16 07:34:51,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d5fd4da-f283-4b87-ba80-eb751b0de132/OceanDNA-b31542.fa --refList OceanDNA-b31542/target_genomes.txt --output OceanDNA-b31542/fastani_result.tsv --threads 1
[2023-03-16 07:34:57,896] [INFO] Task succeeded: fastANI
[2023-03-16 07:34:57,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:34:57,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:34:57,905] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:34:57,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:34:57,905] [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 gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.7769	231	457	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.7447	244	457	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.6155	229	457	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.5938	200	457	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.5932	234	457	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	78.3662	228	457	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.2178	229	457	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.1227	222	457	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.1037	218	457	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	77.97	175	457	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	77.8799	177	457	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7086	183	457	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:34:57,905] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31542/tc_result.tsv
[2023-03-16 07:34:57,905] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:34:57,905] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:34:57,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/checkm_data
[2023-03-16 07:34:57,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:34:57,910] [INFO] Task started: CheckM
[2023-03-16 07:34:57,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31542/checkm_input OceanDNA-b31542/checkm_result
[2023-03-16 07:35:23,998] [INFO] Task succeeded: CheckM
[2023-03-16 07:35:23,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:35:24,003] [INFO] ===== Completeness check finished =====
[2023-03-16 07:35:24,003] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:35:24,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31542/markers.fasta)
[2023-03-16 07:35:24,004] [INFO] Task started: Blastn
[2023-03-16 07:35:24,005] [INFO] Running command: blastn -query OceanDNA-b31542/markers.fasta -db /var/lib/cwl/stg1efd7c4c-fb29-4771-bfca-b4fddb87747f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:24,788] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:24,789] [INFO] Selected 12 target genomes.
[2023-03-16 07:35:24,789] [INFO] Target genome list was writen to OceanDNA-b31542/target_genomes_gtdb.txt
[2023-03-16 07:35:25,153] [INFO] Task started: fastANI
[2023-03-16 07:35:25,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d5fd4da-f283-4b87-ba80-eb751b0de132/OceanDNA-b31542.fa --refList OceanDNA-b31542/target_genomes_gtdb.txt --output OceanDNA-b31542/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:35:31,370] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:31,378] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:35:31,378] [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_009827535.1	s__Altererythrobacter_F oceanensis	98.261	430	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827515.1	s__Pelagerythrobacter marinus	78.7805	242	457	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	78.7586	232	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.586	201	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	78.5758	224	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_000181515.1	s__Qipengyuania sp000181515	78.4665	221	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.1176	223	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	78.0875	219	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	78.0786	207	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	77.9688	170	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441535.1	s__Tsuneonella troitsensis	77.8799	177	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011054555.1	s__Erythrobacter sp011054555	77.8536	168	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:35:31,383] [INFO] GTDB search result was written to OceanDNA-b31542/result_gtdb.tsv
[2023-03-16 07:35:31,392] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:35:31,398] [INFO] DFAST_QC result json was written to OceanDNA-b31542/dqc_result.json
[2023-03-16 07:35:31,398] [INFO] DFAST_QC completed!
[2023-03-16 07:35:31,398] [INFO] Total running time: 0h0m51s