[2023-03-15 20:49:38,745] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:49:38,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:49:38,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference
[2023-03-15 20:49:39,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:49:39,891] [INFO] Task started: Prodigal
[2023-03-15 20:49:39,892] [INFO] Running command: cat /var/lib/cwl/stgc166c42e-df9f-48ff-ad64-c1c0cc8f7f59/OceanDNA-b41426.fa | prodigal -d OceanDNA-b41426/cds.fna -a OceanDNA-b41426/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:50:04,147] [INFO] Task succeeded: Prodigal
[2023-03-15 20:50:04,147] [INFO] Task started: HMMsearch
[2023-03-15 20:50:04,147] [INFO] Running command: hmmsearch --tblout OceanDNA-b41426/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/reference_markers.hmm OceanDNA-b41426/protein.faa > /dev/null
[2023-03-15 20:50:04,369] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:50:04,370] [INFO] Found 6/6 markers.
[2023-03-15 20:50:04,394] [INFO] Query marker FASTA was written to OceanDNA-b41426/markers.fasta
[2023-03-15 20:50:04,394] [INFO] Task started: Blastn
[2023-03-15 20:50:04,394] [INFO] Running command: blastn -query OceanDNA-b41426/markers.fasta -db /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/reference_markers.fasta -out OceanDNA-b41426/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:50:05,093] [INFO] Task succeeded: Blastn
[2023-03-15 20:50:05,094] [INFO] Selected 19 target genomes.
[2023-03-15 20:50:05,094] [INFO] Target genome list was writen to OceanDNA-b41426/target_genomes.txt
[2023-03-15 20:50:05,105] [INFO] Task started: fastANI
[2023-03-15 20:50:05,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgc166c42e-df9f-48ff-ad64-c1c0cc8f7f59/OceanDNA-b41426.fa --refList OceanDNA-b41426/target_genomes.txt --output OceanDNA-b41426/fastani_result.tsv --threads 1
[2023-03-15 20:50:17,450] [INFO] Task succeeded: fastANI
[2023-03-15 20:50:17,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:50:17,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:50:17,458] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:50:17,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:50:17,458] [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
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.7652	476	1362	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.9692	186	1362	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.7948	134	1362	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.7815	239	1362	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.6696	247	1362	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.5862	174	1362	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	76.4421	55	1362	95	below_threshold
Marinospirillum alkaliphilum	strain=DSM 21637	GCA_900119735.1	148454	148454	type	True	75.8336	62	1362	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	75.3961	65	1362	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	75.375	65	1362	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:50:17,458] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41426/tc_result.tsv
[2023-03-15 20:50:17,458] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:50:17,458] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:50:17,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/checkm_data
[2023-03-15 20:50:17,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:50:17,464] [INFO] Task started: CheckM
[2023-03-15 20:50:17,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41426/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41426/checkm_input OceanDNA-b41426/checkm_result
[2023-03-15 20:51:18,002] [INFO] Task succeeded: CheckM
[2023-03-15 20:51:18,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:51:18,005] [INFO] ===== Completeness check finished =====
[2023-03-15 20:51:18,005] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:51:18,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41426/markers.fasta)
[2023-03-15 20:51:18,007] [INFO] Task started: Blastn
[2023-03-15 20:51:18,007] [INFO] Running command: blastn -query OceanDNA-b41426/markers.fasta -db /var/lib/cwl/stg803243a3-62ba-40ef-83be-2ecdb2d2a59c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41426/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:51:19,190] [INFO] Task succeeded: Blastn
[2023-03-15 20:51:19,241] [INFO] Selected 8 target genomes.
[2023-03-15 20:51:19,242] [INFO] Target genome list was writen to OceanDNA-b41426/target_genomes_gtdb.txt
[2023-03-15 20:51:19,486] [INFO] Task started: fastANI
[2023-03-15 20:51:19,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgc166c42e-df9f-48ff-ad64-c1c0cc8f7f59/OceanDNA-b41426.fa --refList OceanDNA-b41426/target_genomes_gtdb.txt --output OceanDNA-b41426/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:51:26,403] [INFO] Task succeeded: fastANI
[2023-03-15 20:51:26,409] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:51:26,409] [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
GCA_002314145.1	s__UBA2009 sp002314145	99.9897	1319	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	conclusive
GCA_002706025.1	s__UBA2009 sp002706025	81.317	808	1362	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_007785795.1	s__UBA2009 sp002335285	78.8281	510	1362	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_002733205.1	s__UBA2009 sp002733205	78.678	432	1362	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_016132445.1	s__UBA2009 sp016132445	78.5463	366	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCF_000355675.1	s__Thalassolituus oleivorans	77.7879	135	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCF_000422845.1	s__Oceanobacter kriegii	77.7781	240	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	76.9969	130	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:51:26,409] [INFO] GTDB search result was written to OceanDNA-b41426/result_gtdb.tsv
[2023-03-15 20:51:26,409] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:51:26,411] [INFO] DFAST_QC result json was written to OceanDNA-b41426/dqc_result.json
[2023-03-15 20:51:26,411] [INFO] DFAST_QC completed!
[2023-03-15 20:51:26,411] [INFO] Total running time: 0h1m48s