[2023-03-15 13:03:53,430] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,431] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference
[2023-03-15 13:03:54,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,640] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,640] [INFO] Running command: cat /var/lib/cwl/stg062cccc8-d263-4a39-b4c9-b53056244e72/OceanDNA-b34568.fa | prodigal -d OceanDNA-b34568/cds.fna -a OceanDNA-b34568/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:12,124] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:12,124] [INFO] Task started: HMMsearch
[2023-03-15 13:04:12,124] [INFO] Running command: hmmsearch --tblout OceanDNA-b34568/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/reference_markers.hmm OceanDNA-b34568/protein.faa > /dev/null
[2023-03-15 13:04:12,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:12,400] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg062cccc8-d263-4a39-b4c9-b53056244e72/OceanDNA-b34568.fa]
[2023-03-15 13:04:12,424] [INFO] Query marker FASTA was written to OceanDNA-b34568/markers.fasta
[2023-03-15 13:04:12,424] [INFO] Task started: Blastn
[2023-03-15 13:04:12,424] [INFO] Running command: blastn -query OceanDNA-b34568/markers.fasta -db /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/reference_markers.fasta -out OceanDNA-b34568/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:12,997] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:12,997] [INFO] Selected 21 target genomes.
[2023-03-15 13:04:12,998] [INFO] Target genome list was writen to OceanDNA-b34568/target_genomes.txt
[2023-03-15 13:04:13,011] [INFO] Task started: fastANI
[2023-03-15 13:04:13,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg062cccc8-d263-4a39-b4c9-b53056244e72/OceanDNA-b34568.fa --refList OceanDNA-b34568/target_genomes.txt --output OceanDNA-b34568/fastani_result.tsv --threads 1
[2023-03-15 13:04:28,824] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:28,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:28,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:28,832] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:28,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:04:28,832] [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
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	86.5795	823	999	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	86.4857	798	999	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	80.9345	528	999	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	80.9167	529	999	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.6283	137	999	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.4037	76	999	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.0861	103	999	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.0495	129	999	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.0177	69	999	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	76.9346	82	999	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	76.8397	68	999	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:28,833] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34568/tc_result.tsv
[2023-03-15 13:04:28,833] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:28,833] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:28,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/checkm_data
[2023-03-15 13:04:28,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:28,839] [INFO] Task started: CheckM
[2023-03-15 13:04:28,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34568/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34568/checkm_input OceanDNA-b34568/checkm_result
[2023-03-15 13:05:14,420] [INFO] Task succeeded: CheckM
[2023-03-15 13:05:14,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:05:14,423] [INFO] ===== Completeness check finished =====
[2023-03-15 13:05:14,423] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:05:14,423] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34568/markers.fasta)
[2023-03-15 13:05:14,424] [INFO] Task started: Blastn
[2023-03-15 13:05:14,424] [INFO] Running command: blastn -query OceanDNA-b34568/markers.fasta -db /var/lib/cwl/stg954fabf8-7a9d-4bb7-8bb3-b7ff962fd09c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34568/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:05:15,191] [INFO] Task succeeded: Blastn
[2023-03-15 13:05:15,191] [INFO] Selected 7 target genomes.
[2023-03-15 13:05:15,192] [INFO] Target genome list was writen to OceanDNA-b34568/target_genomes_gtdb.txt
[2023-03-15 13:05:15,239] [INFO] Task started: fastANI
[2023-03-15 13:05:15,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg062cccc8-d263-4a39-b4c9-b53056244e72/OceanDNA-b34568.fa --refList OceanDNA-b34568/target_genomes_gtdb.txt --output OceanDNA-b34568/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:21,084] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:21,089] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:05:21,089] [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_003731635.1	s__Alteromonas oceani	86.5648	824	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	86.4904	797	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	86.2348	768	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCA_002691625.1	s__Alteromonas sp002691625	86.1956	673	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCA_018222405.1	s__Alteromonas sp018222405	85.974	848	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	80.9345	528	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005222225.1	s__Alteromonas lutimaris	77.0495	129	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:21,090] [INFO] GTDB search result was written to OceanDNA-b34568/result_gtdb.tsv
[2023-03-15 13:05:21,090] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:21,091] [INFO] DFAST_QC result json was written to OceanDNA-b34568/dqc_result.json
[2023-03-15 13:05:21,091] [INFO] DFAST_QC completed!
[2023-03-15 13:05:21,091] [INFO] Total running time: 0h1m28s