[2023-03-15 20:34:28,082] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:28,082] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:28,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference
[2023-03-15 20:34:29,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:29,168] [INFO] Task started: Prodigal
[2023-03-15 20:34:29,168] [INFO] Running command: cat /var/lib/cwl/stg2cf2dc3b-648d-4e0f-b0b2-6763339687cd/OceanDNA-b41182.fa | prodigal -d OceanDNA-b41182/cds.fna -a OceanDNA-b41182/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:54,002] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:54,002] [INFO] Task started: HMMsearch
[2023-03-15 20:34:54,002] [INFO] Running command: hmmsearch --tblout OceanDNA-b41182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/reference_markers.hmm OceanDNA-b41182/protein.faa > /dev/null
[2023-03-15 20:34:54,215] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:54,216] [INFO] Found 6/6 markers.
[2023-03-15 20:34:54,241] [INFO] Query marker FASTA was written to OceanDNA-b41182/markers.fasta
[2023-03-15 20:34:54,241] [INFO] Task started: Blastn
[2023-03-15 20:34:54,241] [INFO] Running command: blastn -query OceanDNA-b41182/markers.fasta -db /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/reference_markers.fasta -out OceanDNA-b41182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:55,049] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:55,050] [INFO] Selected 24 target genomes.
[2023-03-15 20:34:55,050] [INFO] Target genome list was writen to OceanDNA-b41182/target_genomes.txt
[2023-03-15 20:34:55,063] [INFO] Task started: fastANI
[2023-03-15 20:34:55,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf2dc3b-648d-4e0f-b0b2-6763339687cd/OceanDNA-b41182.fa --refList OceanDNA-b41182/target_genomes.txt --output OceanDNA-b41182/fastani_result.tsv --threads 1
[2023-03-15 20:35:12,842] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:12,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:12,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:12,855] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:12,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:35:12,855] [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	79.5927	559	1347	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.5549	544	1347	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	79.4459	546	1347	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.3945	566	1347	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	79.3715	565	1347	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	79.3484	539	1347	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.3333	309	1347	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.2843	304	1347	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.2182	328	1347	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.182	323	1347	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.0744	314	1347	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	77.9473	318	1347	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	77.8515	319	1347	95	below_threshold
Pseudomonas marincola	strain=JCM 14761	GCA_900116605.1	437900	437900	type	True	77.1805	162	1347	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.0622	200	1347	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	77.0609	146	1347	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	77.0539	153	1347	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	77.016	192	1347	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9743	227	1347	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	76.8055	165	1347	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	76.5697	175	1347	95	below_threshold
Pseudomonas nabeulensis	strain=E10B	GCA_004682045.1	2293833	2293833	type	True	76.5018	145	1347	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.2893	62	1347	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:35:12,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41182/tc_result.tsv
[2023-03-15 20:35:12,855] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:12,856] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:12,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/checkm_data
[2023-03-15 20:35:12,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:12,861] [INFO] Task started: CheckM
[2023-03-15 20:35:12,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41182/checkm_input OceanDNA-b41182/checkm_result
[2023-03-15 20:36:13,760] [INFO] Task succeeded: CheckM
[2023-03-15 20:36:13,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:36:13,763] [INFO] ===== Completeness check finished =====
[2023-03-15 20:36:13,763] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:36:13,763] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41182/markers.fasta)
[2023-03-15 20:36:13,763] [INFO] Task started: Blastn
[2023-03-15 20:36:13,763] [INFO] Running command: blastn -query OceanDNA-b41182/markers.fasta -db /var/lib/cwl/stg1dd2ceb9-fc27-4ade-b397-382d7381fbf4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:36:15,307] [INFO] Task succeeded: Blastn
[2023-03-15 20:36:15,308] [INFO] Selected 19 target genomes.
[2023-03-15 20:36:15,308] [INFO] Target genome list was writen to OceanDNA-b41182/target_genomes_gtdb.txt
[2023-03-15 20:36:15,604] [INFO] Task started: fastANI
[2023-03-15 20:36:15,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf2dc3b-648d-4e0f-b0b2-6763339687cd/OceanDNA-b41182.fa --refList OceanDNA-b41182/target_genomes_gtdb.txt --output OceanDNA-b41182/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:36:29,990] [INFO] Task succeeded: fastANI
[2023-03-15 20:36:30,001] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:36:30,001] [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_003797905.1	s__Pseudomonas_D sp002683975	98.6082	1213	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	conclusive
GCA_011053055.1	s__Pseudomonas_D sabulinigri_A	81.5286	785	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.96	99.96	0.96	0.96	2	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	81.4404	815	1347	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_003444685.1	s__Pseudomonas_D gallaeciensis	79.7216	560	1347	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_900114765.1	s__Pseudomonas_D pachastrellae	79.5966	559	1347	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_002197985.1	s__Pseudomonas_D aestusnigri	79.3635	566	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	78.908	435	1347	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_009497895.1	s__Pseudomonas_D pelagia_A	78.7548	407	1347	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	78.4172	369	1347	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	78.2783	203	1347	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	78.2593	318	1347	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	78.2368	301	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	78.224	274	1347	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_900114735.1	s__Pseudomonas_D bauzanensis	78.1923	323	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	77.7525	253	1347	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_900116605.1	s__Pseudomonas_E marincola	77.1786	163	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.48	97.31	0.90	0.86	9	-
GCF_012975065.1	s__Pseudomonas_E sp012975065	77.1158	167	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCF_018704125.1	s__Pseudomonas_F sp018704125	76.99	177	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	76.9262	236	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
--------------------------------------------------------------------------------
[2023-03-15 20:36:30,001] [INFO] GTDB search result was written to OceanDNA-b41182/result_gtdb.tsv
[2023-03-15 20:36:30,001] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:36:30,004] [INFO] DFAST_QC result json was written to OceanDNA-b41182/dqc_result.json
[2023-03-15 20:36:30,004] [INFO] DFAST_QC completed!
[2023-03-15 20:36:30,004] [INFO] Total running time: 0h2m2s