[2023-03-15 08:15:08,380] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:15:08,380] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:15:08,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference
[2023-03-15 08:15:09,468] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:15:09,469] [INFO] Task started: Prodigal
[2023-03-15 08:15:09,469] [INFO] Running command: cat /var/lib/cwl/stgc39f77c1-a2f8-4985-9c33-b8abe71e32a7/OceanDNA-b31695.fa | prodigal -d OceanDNA-b31695/cds.fna -a OceanDNA-b31695/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:15:17,525] [INFO] Task succeeded: Prodigal
[2023-03-15 08:15:17,526] [INFO] Task started: HMMsearch
[2023-03-15 08:15:17,526] [INFO] Running command: hmmsearch --tblout OceanDNA-b31695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/reference_markers.hmm OceanDNA-b31695/protein.faa > /dev/null
[2023-03-15 08:15:17,676] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:15:17,676] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc39f77c1-a2f8-4985-9c33-b8abe71e32a7/OceanDNA-b31695.fa]
[2023-03-15 08:15:17,692] [INFO] Query marker FASTA was written to OceanDNA-b31695/markers.fasta
[2023-03-15 08:15:17,693] [INFO] Task started: Blastn
[2023-03-15 08:15:17,693] [INFO] Running command: blastn -query OceanDNA-b31695/markers.fasta -db /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/reference_markers.fasta -out OceanDNA-b31695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:15:18,320] [INFO] Task succeeded: Blastn
[2023-03-15 08:15:18,321] [INFO] Selected 15 target genomes.
[2023-03-15 08:15:18,321] [INFO] Target genome list was writen to OceanDNA-b31695/target_genomes.txt
[2023-03-15 08:15:18,331] [INFO] Task started: fastANI
[2023-03-15 08:15:18,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39f77c1-a2f8-4985-9c33-b8abe71e32a7/OceanDNA-b31695.fa --refList OceanDNA-b31695/target_genomes.txt --output OceanDNA-b31695/fastani_result.tsv --threads 1
[2023-03-15 08:15:26,252] [INFO] Task succeeded: fastANI
[2023-03-15 08:15:26,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:15:26,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:15:26,262] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:15:26,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:15:26,262] [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 pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.1332	228	361	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.5706	214	361	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.5325	203	361	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.5176	209	361	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.2787	184	361	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.2582	182	361	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.0396	184	361	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.0331	197	361	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.9525	184	361	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.9114	161	361	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.9039	175	361	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.7825	176	361	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.6617	195	361	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.4913	179	361	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.365	165	361	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:15:26,262] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31695/tc_result.tsv
[2023-03-15 08:15:26,262] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:15:26,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:15:26,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/checkm_data
[2023-03-15 08:15:26,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:15:26,267] [INFO] Task started: CheckM
[2023-03-15 08:15:26,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31695/checkm_input OceanDNA-b31695/checkm_result
[2023-03-15 08:15:51,219] [INFO] Task succeeded: CheckM
[2023-03-15 08:15:51,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.62%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:15:51,243] [INFO] ===== Completeness check finished =====
[2023-03-15 08:15:51,243] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:15:51,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31695/markers.fasta)
[2023-03-15 08:15:51,244] [INFO] Task started: Blastn
[2023-03-15 08:15:51,244] [INFO] Running command: blastn -query OceanDNA-b31695/markers.fasta -db /var/lib/cwl/stg9152233d-4421-4d2e-9928-da248dbd5b94/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:15:52,060] [INFO] Task succeeded: Blastn
[2023-03-15 08:15:52,068] [INFO] Selected 12 target genomes.
[2023-03-15 08:15:52,068] [INFO] Target genome list was writen to OceanDNA-b31695/target_genomes_gtdb.txt
[2023-03-15 08:15:52,080] [INFO] Task started: fastANI
[2023-03-15 08:15:52,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39f77c1-a2f8-4985-9c33-b8abe71e32a7/OceanDNA-b31695.fa --refList OceanDNA-b31695/target_genomes_gtdb.txt --output OceanDNA-b31695/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:15:58,487] [INFO] Task succeeded: fastANI
[2023-03-15 08:15:58,494] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:15:58,494] [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
GCA_018819685.1	s__Qipengyuania sp018819685	97.803	296	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	conclusive
GCA_018828205.1	s__Qipengyuania sp018828205	88.0739	278	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	86.4266	297	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	80.1332	228	361	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	80.0033	218	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_011762005.1	s__Qipengyuania flava	79.5176	209	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	79.3707	186	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.0564	196	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911835.1	s__Erythrobacter sp013911835	79.0328	125	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.9816	205	361	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	78.9525	184	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	78.6422	180	361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:15:58,500] [INFO] GTDB search result was written to OceanDNA-b31695/result_gtdb.tsv
[2023-03-15 08:15:58,504] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:15:58,508] [INFO] DFAST_QC result json was written to OceanDNA-b31695/dqc_result.json
[2023-03-15 08:15:58,508] [INFO] DFAST_QC completed!
[2023-03-15 08:15:58,508] [INFO] Total running time: 0h0m50s