[2023-03-16 10:20:34,835] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,835] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference
[2023-03-16 10:20:36,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,113] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,113] [INFO] Running command: cat /var/lib/cwl/stg4e6245e9-d07d-4c29-8347-1002c4d5ae14/OceanDNA-b31537.fa | prodigal -d OceanDNA-b31537/cds.fna -a OceanDNA-b31537/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:55,743] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:55,743] [INFO] Task started: HMMsearch
[2023-03-16 10:20:55,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b31537/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/reference_markers.hmm OceanDNA-b31537/protein.faa > /dev/null
[2023-03-16 10:20:56,060] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:56,060] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4e6245e9-d07d-4c29-8347-1002c4d5ae14/OceanDNA-b31537.fa]
[2023-03-16 10:20:56,080] [INFO] Query marker FASTA was written to OceanDNA-b31537/markers.fasta
[2023-03-16 10:20:56,087] [INFO] Task started: Blastn
[2023-03-16 10:20:56,087] [INFO] Running command: blastn -query OceanDNA-b31537/markers.fasta -db /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/reference_markers.fasta -out OceanDNA-b31537/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:56,836] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:56,836] [INFO] Selected 21 target genomes.
[2023-03-16 10:20:56,837] [INFO] Target genome list was writen to OceanDNA-b31537/target_genomes.txt
[2023-03-16 10:20:56,851] [INFO] Task started: fastANI
[2023-03-16 10:20:56,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e6245e9-d07d-4c29-8347-1002c4d5ae14/OceanDNA-b31537.fa --refList OceanDNA-b31537/target_genomes.txt --output OceanDNA-b31537/fastani_result.tsv --threads 1
[2023-03-16 10:21:09,500] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:09,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:09,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:09,515] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:09,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:09,516] [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
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	81.6261	623	1015	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	79.3176	463	1015	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.0474	343	1015	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.0287	332	1015	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	78.0264	355	1015	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	77.7986	221	1015	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.7386	348	1015	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.7003	315	1015	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.6976	306	1015	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	77.6361	275	1015	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.6243	294	1015	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.6045	294	1015	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.5691	267	1015	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.5683	297	1015	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.5367	312	1015	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.4473	312	1015	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.4007	241	1015	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	77.3981	306	1015	95	below_threshold
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	77.2958	279	1015	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.1496	243	1015	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	76.9776	236	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:09,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31537/tc_result.tsv
[2023-03-16 10:21:09,516] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:09,516] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:09,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/checkm_data
[2023-03-16 10:21:09,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:09,524] [INFO] Task started: CheckM
[2023-03-16 10:21:09,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31537/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31537/checkm_input OceanDNA-b31537/checkm_result
[2023-03-16 10:21:59,118] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:59,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:59,122] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:59,122] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:59,122] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31537/markers.fasta)
[2023-03-16 10:21:59,123] [INFO] Task started: Blastn
[2023-03-16 10:21:59,124] [INFO] Running command: blastn -query OceanDNA-b31537/markers.fasta -db /var/lib/cwl/stg4ea0fa83-c46c-49c2-96c8-eaa81538c19e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31537/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:00,502] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:00,503] [INFO] Selected 17 target genomes.
[2023-03-16 10:22:00,503] [INFO] Target genome list was writen to OceanDNA-b31537/target_genomes_gtdb.txt
[2023-03-16 10:22:00,513] [INFO] Task started: fastANI
[2023-03-16 10:22:00,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e6245e9-d07d-4c29-8347-1002c4d5ae14/OceanDNA-b31537.fa --refList OceanDNA-b31537/target_genomes_gtdb.txt --output OceanDNA-b31537/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:22:10,726] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:10,736] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:22:10,736] [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_009828115.1	s__Pseudopontixanthobacter_A sediminis	81.6145	624	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	79.3176	463	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.2564	378	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_005884405.1	s__Qipengyuania marisflavi	78.2461	356	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.0287	332	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009828095.1	s__Pontixanthobacter luteolus	78.0264	355	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	77.9404	314	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.831	359	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.615	293	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009828025.1	s__Qipengyuania algicida	77.6032	276	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013336795.1	s__Pseudopontixanthobacter muriae	77.5812	275	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	77.5723	305	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590965.1	s__Novosphingobium lentum	77.3977	306	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	77.3537	337	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.2985	297	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827455.1	s__Pontixanthobacter aestiaquae	77.2958	279	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	77.1552	246	1015	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 10:22:10,736] [INFO] GTDB search result was written to OceanDNA-b31537/result_gtdb.tsv
[2023-03-16 10:22:10,736] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:22:10,739] [INFO] DFAST_QC result json was written to OceanDNA-b31537/dqc_result.json
[2023-03-16 10:22:10,739] [INFO] DFAST_QC completed!
[2023-03-16 10:22:10,739] [INFO] Total running time: 0h1m36s