[2023-03-15 15:55:16,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,912] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,912] [INFO] Running command: cat /var/lib/cwl/stg72356696-b7ff-47c3-9854-5e277a3c14aa/OceanDNA-b41015.fa | prodigal -d OceanDNA-b41015/cds.fna -a OceanDNA-b41015/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:39,823] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:39,823] [INFO] Task started: HMMsearch
[2023-03-15 15:55:39,823] [INFO] Running command: hmmsearch --tblout OceanDNA-b41015/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/reference_markers.hmm OceanDNA-b41015/protein.faa > /dev/null
[2023-03-15 15:55:40,049] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:40,049] [INFO] Found 6/6 markers.
[2023-03-15 15:55:40,071] [INFO] Query marker FASTA was written to OceanDNA-b41015/markers.fasta
[2023-03-15 15:55:40,073] [INFO] Task started: Blastn
[2023-03-15 15:55:40,073] [INFO] Running command: blastn -query OceanDNA-b41015/markers.fasta -db /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/reference_markers.fasta -out OceanDNA-b41015/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:40,819] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:40,820] [INFO] Selected 19 target genomes.
[2023-03-15 15:55:40,820] [INFO] Target genome list was writen to OceanDNA-b41015/target_genomes.txt
[2023-03-15 15:55:40,833] [INFO] Task started: fastANI
[2023-03-15 15:55:40,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg72356696-b7ff-47c3-9854-5e277a3c14aa/OceanDNA-b41015.fa --refList OceanDNA-b41015/target_genomes.txt --output OceanDNA-b41015/fastani_result.tsv --threads 1
[2023-03-15 15:55:54,785] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:54,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:54,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:54,798] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:54,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:54,798] [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 pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.7339	500	1177	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.7051	481	1177	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.6555	496	1177	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	78.6542	484	1177	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	78.6448	484	1177	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.6196	493	1177	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	77.9332	252	1177	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	77.7061	262	1177	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	77.6742	261	1177	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	77.6709	270	1177	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	77.5126	277	1177	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.8031	149	1177	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	76.78	153	1177	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.7487	148	1177	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.7464	184	1177	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.7416	170	1177	95	below_threshold
Pseudomonas antarctica		GCA_900624995.1	219572	219572	type	True	76.7278	110	1177	95	below_threshold
Pseudomonas antarctica	strain=CMS 35	GCA_010634845.1	219572	219572	type	True	76.707	114	1177	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	76.5114	118	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:54,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41015/tc_result.tsv
[2023-03-15 15:55:54,799] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:54,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:54,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/checkm_data
[2023-03-15 15:55:54,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:54,805] [INFO] Task started: CheckM
[2023-03-15 15:55:54,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41015/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41015/checkm_input OceanDNA-b41015/checkm_result
[2023-03-15 15:56:49,578] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:49,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:49,581] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:49,581] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:49,581] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41015/markers.fasta)
[2023-03-15 15:56:49,583] [INFO] Task started: Blastn
[2023-03-15 15:56:49,583] [INFO] Running command: blastn -query OceanDNA-b41015/markers.fasta -db /var/lib/cwl/stg70d14556-c0a2-4a76-bb90-53056cc9aed8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41015/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:50,812] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:50,813] [INFO] Selected 14 target genomes.
[2023-03-15 15:56:50,813] [INFO] Target genome list was writen to OceanDNA-b41015/target_genomes_gtdb.txt
[2023-03-15 15:56:50,827] [INFO] Task started: fastANI
[2023-03-15 15:56:50,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg72356696-b7ff-47c3-9854-5e277a3c14aa/OceanDNA-b41015.fa --refList OceanDNA-b41015/target_genomes_gtdb.txt --output OceanDNA-b41015/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:57:01,016] [INFO] Task succeeded: fastANI
[2023-03-15 15:57:01,025] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:57:01,025] [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_011053055.1	s__Pseudomonas_D sabulinigri_A	98.1606	1089	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.96	99.96	0.96	0.96	2	conclusive
GCF_003797905.1	s__Pseudomonas_D sp002683975	81.3087	767	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	81.2297	804	1177	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_900114765.1	s__Pseudomonas_D pachastrellae	78.7282	500	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_002903165.1	s__Pseudomonas_D oceani	78.7104	481	1177	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_003444685.1	s__Pseudomonas_D gallaeciensis	78.6848	486	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	78.6358	491	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	78.1342	344	1177	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_002296055.1	s__Pseudomonas_D sp002296055	78.0842	419	1177	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	77.795	342	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	77.7014	213	1177	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_000410875.1	s__Pseudomonas_D pelagia	77.5463	337	1177	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_014219065.1	s__Pseudomonas_D xiamenensis	77.4322	281	1177	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_007117785.1	s__Pseudomonas_D sp007117785	77.2829	179	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:57:01,026] [INFO] GTDB search result was written to OceanDNA-b41015/result_gtdb.tsv
[2023-03-15 15:57:01,026] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:57:01,028] [INFO] DFAST_QC result json was written to OceanDNA-b41015/dqc_result.json
[2023-03-15 15:57:01,028] [INFO] DFAST_QC completed!
[2023-03-15 15:57:01,028] [INFO] Total running time: 0h1m45s