[2023-03-18 22:53:23,464] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:53:23,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:53:23,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference
[2023-03-18 22:53:25,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:53:25,706] [INFO] Task started: Prodigal
[2023-03-18 22:53:25,707] [INFO] Running command: cat /var/lib/cwl/stgf2970ed4-4f97-42b7-9ee7-61d4705bd8e8/OceanDNA-b41436.fa | prodigal -d OceanDNA-b41436/cds.fna -a OceanDNA-b41436/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:53:47,796] [INFO] Task succeeded: Prodigal
[2023-03-18 22:53:47,797] [INFO] Task started: HMMsearch
[2023-03-18 22:53:47,797] [INFO] Running command: hmmsearch --tblout OceanDNA-b41436/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/reference_markers.hmm OceanDNA-b41436/protein.faa > /dev/null
[2023-03-18 22:53:48,022] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:53:48,023] [INFO] Found 6/6 markers.
[2023-03-18 22:53:48,046] [INFO] Query marker FASTA was written to OceanDNA-b41436/markers.fasta
[2023-03-18 22:53:48,047] [INFO] Task started: Blastn
[2023-03-18 22:53:48,047] [INFO] Running command: blastn -query OceanDNA-b41436/markers.fasta -db /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/reference_markers.fasta -out OceanDNA-b41436/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:53:48,730] [INFO] Task succeeded: Blastn
[2023-03-18 22:53:48,731] [INFO] Selected 25 target genomes.
[2023-03-18 22:53:48,731] [INFO] Target genome list was writen to OceanDNA-b41436/target_genomes.txt
[2023-03-18 22:53:48,771] [INFO] Task started: fastANI
[2023-03-18 22:53:48,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2970ed4-4f97-42b7-9ee7-61d4705bd8e8/OceanDNA-b41436.fa --refList OceanDNA-b41436/target_genomes.txt --output OceanDNA-b41436/fastani_result.tsv --threads 1
[2023-03-18 22:54:05,201] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:05,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:54:05,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:54:05,210] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:54:05,211] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:54:05,211] [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	79.1866	467	1257	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.126	246	1257	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.946	260	1257	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.7962	211	1257	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.4355	132	1257	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	76.835	162	1257	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	76.5188	63	1257	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	76.3901	76	1257	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	76.364	76	1257	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	76.3018	63	1257	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	76.2983	69	1257	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	76.2272	69	1257	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.016	53	1257	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:54:05,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41436/tc_result.tsv
[2023-03-18 22:54:05,211] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:54:05,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:54:05,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/checkm_data
[2023-03-18 22:54:05,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:54:05,217] [INFO] Task started: CheckM
[2023-03-18 22:54:05,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41436/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41436/checkm_input OceanDNA-b41436/checkm_result
[2023-03-18 22:55:01,142] [INFO] Task succeeded: CheckM
[2023-03-18 22:55:01,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:55:01,148] [INFO] ===== Completeness check finished =====
[2023-03-18 22:55:01,148] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:55:01,148] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41436/markers.fasta)
[2023-03-18 22:55:01,149] [INFO] Task started: Blastn
[2023-03-18 22:55:01,149] [INFO] Running command: blastn -query OceanDNA-b41436/markers.fasta -db /var/lib/cwl/stgfdf3267f-6de1-4d82-8d6d-9de1c5ae6fe2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41436/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:55:02,224] [INFO] Task succeeded: Blastn
[2023-03-18 22:55:02,225] [INFO] Selected 10 target genomes.
[2023-03-18 22:55:02,225] [INFO] Target genome list was writen to OceanDNA-b41436/target_genomes_gtdb.txt
[2023-03-18 22:55:02,237] [INFO] Task started: fastANI
[2023-03-18 22:55:02,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2970ed4-4f97-42b7-9ee7-61d4705bd8e8/OceanDNA-b41436.fa --refList OceanDNA-b41436/target_genomes_gtdb.txt --output OceanDNA-b41436/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:55:09,672] [INFO] Task succeeded: fastANI
[2023-03-18 22:55:09,679] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:55:09,679] [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_002706025.1	s__UBA2009 sp002706025	99.2645	1168	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	conclusive
GCA_002314145.1	s__UBA2009 sp002314145	81.3396	808	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCF_007785795.1	s__UBA2009 sp002335285	79.161	463	1257	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	78.8826	409	1257	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	78.5401	343	1257	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_000422845.1	s__Oceanobacter kriegii	78.126	246	1257	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_002237535.1	s__Bacterioplanes sanyensis_A	77.2248	153	1257	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_006212115.1	s__Oleibacter sp006212115	77.1381	146	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683905.1	s__Pseudomonas_E putida_A	75.6854	70	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
--------------------------------------------------------------------------------
[2023-03-18 22:55:09,680] [INFO] GTDB search result was written to OceanDNA-b41436/result_gtdb.tsv
[2023-03-18 22:55:09,682] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:55:09,684] [INFO] DFAST_QC result json was written to OceanDNA-b41436/dqc_result.json
[2023-03-18 22:55:09,684] [INFO] DFAST_QC completed!
[2023-03-18 22:55:09,684] [INFO] Total running time: 0h1m46s