[2023-03-18 23:27:53,706] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference
[2023-03-18 23:27:55,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,548] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stgc3a1c379-e2c3-4507-a946-9cc11a958f60/OceanDNA-b41330.fa | prodigal -d OceanDNA-b41330/cds.fna -a OceanDNA-b41330/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:18,233] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:18,233] [INFO] Task started: HMMsearch
[2023-03-18 23:28:18,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b41330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/reference_markers.hmm OceanDNA-b41330/protein.faa > /dev/null
[2023-03-18 23:28:18,511] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:18,512] [INFO] Found 6/6 markers.
[2023-03-18 23:28:18,534] [INFO] Query marker FASTA was written to OceanDNA-b41330/markers.fasta
[2023-03-18 23:28:18,534] [INFO] Task started: Blastn
[2023-03-18 23:28:18,534] [INFO] Running command: blastn -query OceanDNA-b41330/markers.fasta -db /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/reference_markers.fasta -out OceanDNA-b41330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:19,214] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:19,215] [INFO] Selected 28 target genomes.
[2023-03-18 23:28:19,215] [INFO] Target genome list was writen to OceanDNA-b41330/target_genomes.txt
[2023-03-18 23:28:19,240] [INFO] Task started: fastANI
[2023-03-18 23:28:19,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a1c379-e2c3-4507-a946-9cc11a958f60/OceanDNA-b41330.fa --refList OceanDNA-b41330/target_genomes.txt --output OceanDNA-b41330/fastani_result.tsv --threads 1
[2023-03-18 23:28:37,167] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:37,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:37,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:37,173] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:37,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:37,174] [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
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	78.2326	456	1189	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.1729	393	1189	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	77.4501	169	1189	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.2402	116	1189	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.1889	143	1189	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	76.1635	66	1189	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	75.6246	51	1189	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:37,174] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41330/tc_result.tsv
[2023-03-18 23:28:37,174] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:37,174] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:37,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/checkm_data
[2023-03-18 23:28:37,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:37,246] [INFO] Task started: CheckM
[2023-03-18 23:28:37,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41330/checkm_input OceanDNA-b41330/checkm_result
[2023-03-18 23:29:32,959] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:32,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:32,981] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:32,982] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:32,982] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41330/markers.fasta)
[2023-03-18 23:29:32,983] [INFO] Task started: Blastn
[2023-03-18 23:29:32,983] [INFO] Running command: blastn -query OceanDNA-b41330/markers.fasta -db /var/lib/cwl/stg7dd1fc97-0e87-4838-b148-a78caca609bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:34,124] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:34,125] [INFO] Selected 19 target genomes.
[2023-03-18 23:29:34,125] [INFO] Target genome list was writen to OceanDNA-b41330/target_genomes_gtdb.txt
[2023-03-18 23:29:34,830] [INFO] Task started: fastANI
[2023-03-18 23:29:34,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a1c379-e2c3-4507-a946-9cc11a958f60/OceanDNA-b41330.fa --refList OceanDNA-b41330/target_genomes_gtdb.txt --output OceanDNA-b41330/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:47,283] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:47,290] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:29:47,290] [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_000422845.1	s__Oceanobacter kriegii	78.1826	392	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785795.1	s__UBA2009 sp002335285	77.6777	215	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002314145.1	s__UBA2009 sp002314145	77.6526	179	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCA_002733205.1	s__UBA2009 sp002733205	77.5462	207	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_002723385.1	s__Oceanobacter sp002723385	77.5446	204	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	99.82	99.82	0.84	0.84	2	-
GCA_002298335.1	s__Oleibacter sp002298335	77.2696	147	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
GCF_900156675.1	s__Oleibacter marinus	77.2402	116	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCF_014652515.1	s__Bacterioplanes sanyensis	77.1889	143	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016132445.1	s__UBA2009 sp016132445	77.1654	189	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_002706025.1	s__UBA2009 sp002706025	77.161	180	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCF_002237535.1	s__Bacterioplanes sanyensis_A	77.1206	130	1189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:47,291] [INFO] GTDB search result was written to OceanDNA-b41330/result_gtdb.tsv
[2023-03-18 23:29:47,291] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:47,292] [INFO] DFAST_QC result json was written to OceanDNA-b41330/dqc_result.json
[2023-03-18 23:29:47,292] [INFO] DFAST_QC completed!
[2023-03-18 23:29:47,292] [INFO] Total running time: 0h1m54s