[2023-03-19 03:22:59,842] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,843] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,843] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference
[2023-03-19 03:23:00,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:00,985] [INFO] Task started: Prodigal
[2023-03-19 03:23:00,985] [INFO] Running command: cat /var/lib/cwl/stg98b4d6b3-e1b7-449c-ad5b-491f0bc02afd/OceanDNA-b31830.fa | prodigal -d OceanDNA-b31830/cds.fna -a OceanDNA-b31830/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:19,446] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:19,447] [INFO] Task started: HMMsearch
[2023-03-19 03:23:19,447] [INFO] Running command: hmmsearch --tblout OceanDNA-b31830/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/reference_markers.hmm OceanDNA-b31830/protein.faa > /dev/null
[2023-03-19 03:23:19,655] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:19,656] [INFO] Found 6/6 markers.
[2023-03-19 03:23:19,691] [INFO] Query marker FASTA was written to OceanDNA-b31830/markers.fasta
[2023-03-19 03:23:19,692] [INFO] Task started: Blastn
[2023-03-19 03:23:19,692] [INFO] Running command: blastn -query OceanDNA-b31830/markers.fasta -db /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/reference_markers.fasta -out OceanDNA-b31830/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:20,583] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:20,602] [INFO] Selected 20 target genomes.
[2023-03-19 03:23:20,602] [INFO] Target genome list was writen to OceanDNA-b31830/target_genomes.txt
[2023-03-19 03:23:20,613] [INFO] Task started: fastANI
[2023-03-19 03:23:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b4d6b3-e1b7-449c-ad5b-491f0bc02afd/OceanDNA-b31830.fa --refList OceanDNA-b31830/target_genomes.txt --output OceanDNA-b31830/fastani_result.tsv --threads 1
[2023-03-19 03:23:32,507] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:32,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:32,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:32,519] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:32,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:23:32,520] [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	87.385	790	994	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.4652	515	994	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.4001	495	994	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	80.1539	384	994	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.1296	502	994	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	80.0002	444	994	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.9378	487	994	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.8307	447	994	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.7612	467	994	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.7216	420	994	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.4364	427	994	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.3598	430	994	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.2642	432	994	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	79.0817	410	994	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.0594	418	994	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.0048	426	994	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.9339	358	994	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	78.6248	379	994	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	78.6137	378	994	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.1112	316	994	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:23:32,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31830/tc_result.tsv
[2023-03-19 03:23:32,524] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:32,525] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:32,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/checkm_data
[2023-03-19 03:23:32,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:32,545] [INFO] Task started: CheckM
[2023-03-19 03:23:32,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31830/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31830/checkm_input OceanDNA-b31830/checkm_result
[2023-03-19 03:24:19,274] [INFO] Task succeeded: CheckM
[2023-03-19 03:24:19,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:24:19,291] [INFO] ===== Completeness check finished =====
[2023-03-19 03:24:19,291] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:24:19,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31830/markers.fasta)
[2023-03-19 03:24:19,293] [INFO] Task started: Blastn
[2023-03-19 03:24:19,293] [INFO] Running command: blastn -query OceanDNA-b31830/markers.fasta -db /var/lib/cwl/stgbd2d5418-e0b6-4e9d-8e14-e2fa73dcd377/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31830/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:24:21,012] [INFO] Task succeeded: Blastn
[2023-03-19 03:24:21,016] [INFO] Selected 15 target genomes.
[2023-03-19 03:24:21,016] [INFO] Target genome list was writen to OceanDNA-b31830/target_genomes_gtdb.txt
[2023-03-19 03:24:21,099] [INFO] Task started: fastANI
[2023-03-19 03:24:21,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b4d6b3-e1b7-449c-ad5b-491f0bc02afd/OceanDNA-b31830.fa --refList OceanDNA-b31830/target_genomes_gtdb.txt --output OceanDNA-b31830/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:24:30,800] [INFO] Task succeeded: fastANI
[2023-03-19 03:24:30,809] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:24:30,809] [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	99.8151	918	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	conclusive
GCA_009993605.1	s__Qipengyuania sp009993605	87.7819	770	994	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	87.385	790	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.9529	549	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009827515.1	s__Pelagerythrobacter marinus	80.3997	495	994	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	80.1285	503	994	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	80.079	461	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.9706	398	994	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	79.9365	532	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.9101	445	994	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_018819685.1	s__Qipengyuania sp018819685	79.5769	364	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.4589	364	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.2697	432	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.7924	365	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	78.0996	317	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:24:30,811] [INFO] GTDB search result was written to OceanDNA-b31830/result_gtdb.tsv
[2023-03-19 03:24:30,814] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:24:30,818] [INFO] DFAST_QC result json was written to OceanDNA-b31830/dqc_result.json
[2023-03-19 03:24:30,818] [INFO] DFAST_QC completed!
[2023-03-19 03:24:30,818] [INFO] Total running time: 0h1m31s