[2023-03-15 07:52:40,258] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,258] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference
[2023-03-15 07:52:41,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,530] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,530] [INFO] Running command: cat /var/lib/cwl/stg4301637e-faa0-4e92-a327-db3f96a79e0e/OceanDNA-b31698.fa | prodigal -d OceanDNA-b31698/cds.fna -a OceanDNA-b31698/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:58,592] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:58,592] [INFO] Task started: HMMsearch
[2023-03-15 07:52:58,593] [INFO] Running command: hmmsearch --tblout OceanDNA-b31698/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/reference_markers.hmm OceanDNA-b31698/protein.faa > /dev/null
[2023-03-15 07:52:58,823] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:58,823] [INFO] Found 6/6 markers.
[2023-03-15 07:52:58,841] [INFO] Query marker FASTA was written to OceanDNA-b31698/markers.fasta
[2023-03-15 07:52:58,842] [INFO] Task started: Blastn
[2023-03-15 07:52:58,842] [INFO] Running command: blastn -query OceanDNA-b31698/markers.fasta -db /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/reference_markers.fasta -out OceanDNA-b31698/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:59,734] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:59,735] [INFO] Selected 23 target genomes.
[2023-03-15 07:52:59,735] [INFO] Target genome list was writen to OceanDNA-b31698/target_genomes.txt
[2023-03-15 07:52:59,748] [INFO] Task started: fastANI
[2023-03-15 07:52:59,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg4301637e-faa0-4e92-a327-db3f96a79e0e/OceanDNA-b31698.fa --refList OceanDNA-b31698/target_genomes.txt --output OceanDNA-b31698/fastani_result.tsv --threads 1
[2023-03-15 07:53:13,429] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:13,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:13,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:13,442] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:13,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:13,443] [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	87.023	742	910	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.1343	497	910	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.9499	487	910	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.8359	484	910	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.7323	447	910	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.6801	461	910	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.6376	440	910	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.489	445	910	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.4614	435	910	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.4136	400	910	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.3917	432	910	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.3145	435	910	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.2267	402	910	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.9931	354	910	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.9914	412	910	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.8972	378	910	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	78.8202	393	910	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.8082	393	910	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.8021	399	910	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.7713	396	910	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	78.3588	357	910	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	78.3522	358	910	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.1593	334	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:13,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31698/tc_result.tsv
[2023-03-15 07:53:13,443] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:13,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:13,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/checkm_data
[2023-03-15 07:53:13,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:13,527] [INFO] Task started: CheckM
[2023-03-15 07:53:13,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31698/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31698/checkm_input OceanDNA-b31698/checkm_result
[2023-03-15 07:53:56,390] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:56,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.28%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:56,393] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:56,393] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:56,393] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31698/markers.fasta)
[2023-03-15 07:53:56,394] [INFO] Task started: Blastn
[2023-03-15 07:53:56,394] [INFO] Running command: blastn -query OceanDNA-b31698/markers.fasta -db /var/lib/cwl/stg9da18726-7f77-43e5-bc87-e354f62385f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31698/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:58,094] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:58,095] [INFO] Selected 16 target genomes.
[2023-03-15 07:53:58,095] [INFO] Target genome list was writen to OceanDNA-b31698/target_genomes_gtdb.txt
[2023-03-15 07:53:58,109] [INFO] Task started: fastANI
[2023-03-15 07:53:58,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg4301637e-faa0-4e92-a327-db3f96a79e0e/OceanDNA-b31698.fa --refList OceanDNA-b31698/target_genomes_gtdb.txt --output OceanDNA-b31698/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:07,574] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:07,584] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:54:07,584] [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_001635685.1	s__Qipengyuania sp001635685	94.0183	740	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCA_009993605.1	s__Qipengyuania sp009993605	87.7829	735	910	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	87.023	742	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	80.1326	430	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.0199	376	910	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	79.8746	514	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.8142	486	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	79.5815	437	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.5486	367	910	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	79.4943	445	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	79.3006	363	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.0981	408	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.748	307	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.6567	348	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.5329	326	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013370205.1	s__Actirhodobacter atriluteus	78.3706	359	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:07,584] [INFO] GTDB search result was written to OceanDNA-b31698/result_gtdb.tsv
[2023-03-15 07:54:07,584] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:07,587] [INFO] DFAST_QC result json was written to OceanDNA-b31698/dqc_result.json
[2023-03-15 07:54:07,587] [INFO] DFAST_QC completed!
[2023-03-15 07:54:07,587] [INFO] Total running time: 0h1m27s