[2023-03-14 12:25:41,464] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference
[2023-03-14 12:25:42,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,659] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,659] [INFO] Running command: cat /var/lib/cwl/stgdfcf1b3a-7257-4223-b02c-ef89933515b9/OceanDNA-b41044.fa | prodigal -d OceanDNA-b41044/cds.fna -a OceanDNA-b41044/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:05,437] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:05,438] [INFO] Task started: HMMsearch
[2023-03-14 12:26:05,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b41044/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/reference_markers.hmm OceanDNA-b41044/protein.faa > /dev/null
[2023-03-14 12:26:05,676] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:05,676] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdfcf1b3a-7257-4223-b02c-ef89933515b9/OceanDNA-b41044.fa]
[2023-03-14 12:26:05,698] [INFO] Query marker FASTA was written to OceanDNA-b41044/markers.fasta
[2023-03-14 12:26:05,698] [INFO] Task started: Blastn
[2023-03-14 12:26:05,698] [INFO] Running command: blastn -query OceanDNA-b41044/markers.fasta -db /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/reference_markers.fasta -out OceanDNA-b41044/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:06,430] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:06,431] [INFO] Selected 20 target genomes.
[2023-03-14 12:26:06,431] [INFO] Target genome list was writen to OceanDNA-b41044/target_genomes.txt
[2023-03-14 12:26:06,445] [INFO] Task started: fastANI
[2023-03-14 12:26:06,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfcf1b3a-7257-4223-b02c-ef89933515b9/OceanDNA-b41044.fa --refList OceanDNA-b41044/target_genomes.txt --output OceanDNA-b41044/fastani_result.tsv --threads 1
[2023-03-14 12:26:22,100] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:22,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:22,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:22,112] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:22,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:22,113] [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=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	83.3553	851	1177	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	83.2961	860	1177	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.6904	284	1177	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.6493	285	1177	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.6377	279	1177	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.4413	283	1177	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.4014	318	1177	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.3684	302	1177	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.3203	308	1177	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.2214	303	1177	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	77.4663	154	1177	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	77.4319	156	1177	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	77.4113	165	1177	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	77.3988	169	1177	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	77.3145	140	1177	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	77.2628	186	1177	95	below_threshold
Pseudomonas marincola	strain=JCM 14761	GCA_900116605.1	437900	437900	type	True	77.2581	136	1177	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	77.249	144	1177	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	77.1364	138	1177	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.9061	146	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:22,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41044/tc_result.tsv
[2023-03-14 12:26:22,113] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:22,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:22,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/checkm_data
[2023-03-14 12:26:22,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:22,144] [INFO] Task started: CheckM
[2023-03-14 12:26:22,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41044/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41044/checkm_input OceanDNA-b41044/checkm_result
[2023-03-14 12:27:19,422] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:19,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:19,425] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:19,426] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:19,426] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41044/markers.fasta)
[2023-03-14 12:27:19,427] [INFO] Task started: Blastn
[2023-03-14 12:27:19,427] [INFO] Running command: blastn -query OceanDNA-b41044/markers.fasta -db /var/lib/cwl/stg962b4d07-3860-4d17-9fc3-f96271ef3e6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41044/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:20,686] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:20,687] [INFO] Selected 8 target genomes.
[2023-03-14 12:27:20,687] [INFO] Target genome list was writen to OceanDNA-b41044/target_genomes_gtdb.txt
[2023-03-14 12:27:20,694] [INFO] Task started: fastANI
[2023-03-14 12:27:20,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfcf1b3a-7257-4223-b02c-ef89933515b9/OceanDNA-b41044.fa --refList OceanDNA-b41044/target_genomes_gtdb.txt --output OceanDNA-b41044/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:26,858] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:26,864] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:26,864] [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_008641105.1	s__Pseudomonas_D salina	83.3694	849	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	81.197	547	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_009497895.1	s__Pseudomonas_D pelagia_A	79.8683	472	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	79.6317	406	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	79.4775	476	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_002840055.1	s__Pseudomonas_D sp002840055	78.9795	273	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_000939975.1	s__Pseudomonas_D saudimassiliensis	78.4813	281	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_002979975.1	s__Pseudomonas_D sp002979975	78.2321	311	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	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:26,864] [INFO] GTDB search result was written to OceanDNA-b41044/result_gtdb.tsv
[2023-03-14 12:27:26,864] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:26,866] [INFO] DFAST_QC result json was written to OceanDNA-b41044/dqc_result.json
[2023-03-14 12:27:26,866] [INFO] DFAST_QC completed!
[2023-03-14 12:27:26,866] [INFO] Total running time: 0h1m45s