[2023-03-15 09:48:16,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,228] [INFO] Running command: cat /var/lib/cwl/stged7e6fec-60d2-4226-8b9d-44897b73f62e/OceanDNA-b41176.fa | prodigal -d OceanDNA-b41176/cds.fna -a OceanDNA-b41176/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:45,696] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:45,696] [INFO] Task started: HMMsearch
[2023-03-15 09:48:45,696] [INFO] Running command: hmmsearch --tblout OceanDNA-b41176/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/reference_markers.hmm OceanDNA-b41176/protein.faa > /dev/null
[2023-03-15 09:48:45,917] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:45,918] [INFO] Found 6/6 markers.
[2023-03-15 09:48:45,944] [INFO] Query marker FASTA was written to OceanDNA-b41176/markers.fasta
[2023-03-15 09:48:45,944] [INFO] Task started: Blastn
[2023-03-15 09:48:45,944] [INFO] Running command: blastn -query OceanDNA-b41176/markers.fasta -db /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/reference_markers.fasta -out OceanDNA-b41176/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:46,757] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:46,758] [INFO] Selected 20 target genomes.
[2023-03-15 09:48:46,758] [INFO] Target genome list was writen to OceanDNA-b41176/target_genomes.txt
[2023-03-15 09:48:46,770] [INFO] Task started: fastANI
[2023-03-15 09:48:46,770] [INFO] Running command: fastANI --query /var/lib/cwl/stged7e6fec-60d2-4226-8b9d-44897b73f62e/OceanDNA-b41176.fa --refList OceanDNA-b41176/target_genomes.txt --output OceanDNA-b41176/fastani_result.tsv --threads 1
[2023-03-15 09:49:01,238] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:01,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:49:01,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:49:01,249] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:49:01,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:49:01,249] [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	79.3142	509	1461	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	79.3057	510	1461	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.1863	394	1461	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.3869	405	1461	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.3727	379	1461	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.3721	403	1461	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.2845	400	1461	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.2767	424	1461	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.2186	423	1461	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	77.9986	394	1461	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.5388	227	1461	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.4925	228	1461	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.3641	231	1461	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.1846	230	1461	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	77.1615	226	1461	95	below_threshold
Pseudomonas massiliensis	strain=CB1	GCA_000826105.1	522492	522492	type	True	76.8093	141	1461	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	76.3352	83	1461	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	76.186	75	1461	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.0683	86	1461	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:49:01,250] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41176/tc_result.tsv
[2023-03-15 09:49:01,250] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:49:01,250] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:49:01,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/checkm_data
[2023-03-15 09:49:01,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:49:01,283] [INFO] Task started: CheckM
[2023-03-15 09:49:01,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41176/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41176/checkm_input OceanDNA-b41176/checkm_result
[2023-03-15 09:50:08,144] [INFO] Task succeeded: CheckM
[2023-03-15 09:50:08,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:50:08,148] [INFO] ===== Completeness check finished =====
[2023-03-15 09:50:08,148] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:50:08,148] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41176/markers.fasta)
[2023-03-15 09:50:08,149] [INFO] Task started: Blastn
[2023-03-15 09:50:08,149] [INFO] Running command: blastn -query OceanDNA-b41176/markers.fasta -db /var/lib/cwl/stg8904a0f4-a030-4e5c-aaf8-928f82c26a96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41176/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:50:09,616] [INFO] Task succeeded: Blastn
[2023-03-15 09:50:09,617] [INFO] Selected 11 target genomes.
[2023-03-15 09:50:09,617] [INFO] Target genome list was writen to OceanDNA-b41176/target_genomes_gtdb.txt
[2023-03-15 09:50:09,839] [INFO] Task started: fastANI
[2023-03-15 09:50:09,839] [INFO] Running command: fastANI --query /var/lib/cwl/stged7e6fec-60d2-4226-8b9d-44897b73f62e/OceanDNA-b41176.fa --refList OceanDNA-b41176/target_genomes_gtdb.txt --output OceanDNA-b41176/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:50:19,164] [INFO] Task succeeded: fastANI
[2023-03-15 09:50:19,171] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:50:19,171] [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_000410875.1	s__Pseudomonas_D pelagia	99.3095	1322	1461	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_008365385.1	s__Pseudomonas_D laoshanensis	83.4001	896	1461	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_009497895.1	s__Pseudomonas_D pelagia_A	83.2373	928	1461	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	79.5879	401	1461	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_008641105.1	s__Pseudomonas_D salina	79.3199	508	1461	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	78.9447	395	1461	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_003797905.1	s__Pseudomonas_D sp002683975	78.7612	370	1461	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	78.6077	431	1461	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	78.268	432	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.2567	304	1461	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_000826105.1	s__Pseudomonas_E massiliensis	76.8342	143	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:50:19,171] [INFO] GTDB search result was written to OceanDNA-b41176/result_gtdb.tsv
[2023-03-15 09:50:19,171] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:50:19,173] [INFO] DFAST_QC result json was written to OceanDNA-b41176/dqc_result.json
[2023-03-15 09:50:19,173] [INFO] DFAST_QC completed!
[2023-03-15 09:50:19,173] [INFO] Total running time: 0h2m3s