[2023-03-15 21:48:07,266] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,266] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference
[2023-03-15 21:48:08,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,885] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,885] [INFO] Running command: cat /var/lib/cwl/stg5e2f0a4d-d168-4c8f-963e-429bea32c440/OceanDNA-b41030.fa | prodigal -d OceanDNA-b41030/cds.fna -a OceanDNA-b41030/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:34,413] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:34,414] [INFO] Task started: HMMsearch
[2023-03-15 21:48:34,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b41030/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/reference_markers.hmm OceanDNA-b41030/protein.faa > /dev/null
[2023-03-15 21:48:34,630] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:34,631] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5e2f0a4d-d168-4c8f-963e-429bea32c440/OceanDNA-b41030.fa]
[2023-03-15 21:48:34,655] [INFO] Query marker FASTA was written to OceanDNA-b41030/markers.fasta
[2023-03-15 21:48:34,656] [INFO] Task started: Blastn
[2023-03-15 21:48:34,656] [INFO] Running command: blastn -query OceanDNA-b41030/markers.fasta -db /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/reference_markers.fasta -out OceanDNA-b41030/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:35,462] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:35,462] [INFO] Selected 17 target genomes.
[2023-03-15 21:48:35,463] [INFO] Target genome list was writen to OceanDNA-b41030/target_genomes.txt
[2023-03-15 21:48:35,474] [INFO] Task started: fastANI
[2023-03-15 21:48:35,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2f0a4d-d168-4c8f-963e-429bea32c440/OceanDNA-b41030.fa --refList OceanDNA-b41030/target_genomes.txt --output OceanDNA-b41030/fastani_result.tsv --threads 1
[2023-03-15 21:48:47,553] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:47,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:47,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:47,563] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:47,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:47,563] [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
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	82.0107	824	1324	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	82.0031	827	1324	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.6844	431	1324	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.5654	439	1324	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.2496	457	1324	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.2485	457	1324	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.0104	480	1324	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.9627	485	1324	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.9399	405	1324	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	78.7845	439	1324	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.7486	436	1324	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.6899	429	1324	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.2176	364	1324	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.084	287	1324	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.0434	293	1324	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.9797	337	1324	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	77.7779	308	1324	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:47,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41030/tc_result.tsv
[2023-03-15 21:48:47,563] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:47,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:47,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/checkm_data
[2023-03-15 21:48:47,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:47,569] [INFO] Task started: CheckM
[2023-03-15 21:48:47,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41030/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41030/checkm_input OceanDNA-b41030/checkm_result
[2023-03-15 21:49:50,599] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:50,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:50,602] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:50,602] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:50,602] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41030/markers.fasta)
[2023-03-15 21:49:50,603] [INFO] Task started: Blastn
[2023-03-15 21:49:50,603] [INFO] Running command: blastn -query OceanDNA-b41030/markers.fasta -db /var/lib/cwl/stg40df96be-49f6-4095-be3d-f65471d7997d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41030/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:52,047] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:52,048] [INFO] Selected 11 target genomes.
[2023-03-15 21:49:52,048] [INFO] Target genome list was writen to OceanDNA-b41030/target_genomes_gtdb.txt
[2023-03-15 21:49:52,109] [INFO] Task started: fastANI
[2023-03-15 21:49:52,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2f0a4d-d168-4c8f-963e-429bea32c440/OceanDNA-b41030.fa --refList OceanDNA-b41030/target_genomes_gtdb.txt --output OceanDNA-b41030/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:00,400] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:00,407] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:50:00,407] [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_016763285.1	s__Pseudomonas_D sp016763285	97.9867	854	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008641105.1	s__Pseudomonas_D salina	81.9942	831	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	80.4756	614	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	80.1734	614	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_000410875.1	s__Pseudomonas_D pelagia	79.9132	574	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	79.6473	404	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.5187	478	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	79.4558	485	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	79.2832	460	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_900114825.1	s__Pseudomonas_D yangmingensis	79.1099	400	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	78.947	486	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:00,407] [INFO] GTDB search result was written to OceanDNA-b41030/result_gtdb.tsv
[2023-03-15 21:50:00,407] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:00,409] [INFO] DFAST_QC result json was written to OceanDNA-b41030/dqc_result.json
[2023-03-15 21:50:00,409] [INFO] DFAST_QC completed!
[2023-03-15 21:50:00,409] [INFO] Total running time: 0h1m53s