[2023-03-15 03:47:39,264] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:47:39,265] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:47:39,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference
[2023-03-15 03:47:45,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:47:45,727] [INFO] Task started: Prodigal
[2023-03-15 03:47:45,727] [INFO] Running command: cat /var/lib/cwl/stge2859802-75c6-4a8a-81bf-c2f26933213d/OceanDNA-b41392.fa | prodigal -d OceanDNA-b41392/cds.fna -a OceanDNA-b41392/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:48:06,807] [INFO] Task succeeded: Prodigal
[2023-03-15 03:48:06,807] [INFO] Task started: HMMsearch
[2023-03-15 03:48:06,807] [INFO] Running command: hmmsearch --tblout OceanDNA-b41392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/reference_markers.hmm OceanDNA-b41392/protein.faa > /dev/null
[2023-03-15 03:48:07,117] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:48:07,118] [INFO] Found 6/6 markers.
[2023-03-15 03:48:07,141] [INFO] Query marker FASTA was written to OceanDNA-b41392/markers.fasta
[2023-03-15 03:48:07,143] [INFO] Task started: Blastn
[2023-03-15 03:48:07,143] [INFO] Running command: blastn -query OceanDNA-b41392/markers.fasta -db /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/reference_markers.fasta -out OceanDNA-b41392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:48:11,090] [INFO] Task succeeded: Blastn
[2023-03-15 03:48:11,090] [INFO] Selected 35 target genomes.
[2023-03-15 03:48:11,091] [INFO] Target genome list was writen to OceanDNA-b41392/target_genomes.txt
[2023-03-15 03:48:11,113] [INFO] Task started: fastANI
[2023-03-15 03:48:11,113] [INFO] Running command: fastANI --query /var/lib/cwl/stge2859802-75c6-4a8a-81bf-c2f26933213d/OceanDNA-b41392.fa --refList OceanDNA-b41392/target_genomes.txt --output OceanDNA-b41392/fastani_result.tsv --threads 1
[2023-03-15 03:48:35,936] [INFO] Task succeeded: fastANI
[2023-03-15 03:48:35,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:48:35,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:48:35,996] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:48:35,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:48:35,996] [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 oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.0489	103	1244	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_000153565.1	207949	207949	type	True	76.5785	61	1244	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	76.5782	64	1244	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	76.55	60	1244	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	76.2551	73	1244	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:48:35,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41392/tc_result.tsv
[2023-03-15 03:48:35,996] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:48:35,996] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:48:35,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/checkm_data
[2023-03-15 03:48:35,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:48:36,002] [INFO] Task started: CheckM
[2023-03-15 03:48:36,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41392/checkm_input OceanDNA-b41392/checkm_result
[2023-03-15 03:49:30,152] [INFO] Task succeeded: CheckM
[2023-03-15 03:49:30,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:49:30,154] [INFO] ===== Completeness check finished =====
[2023-03-15 03:49:30,155] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:49:30,155] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41392/markers.fasta)
[2023-03-15 03:49:30,156] [INFO] Task started: Blastn
[2023-03-15 03:49:30,156] [INFO] Running command: blastn -query OceanDNA-b41392/markers.fasta -db /var/lib/cwl/stg24125c7f-2ed7-4a4f-ba18-81236a2d23c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:49:31,041] [INFO] Task succeeded: Blastn
[2023-03-15 03:49:31,042] [INFO] Selected 17 target genomes.
[2023-03-15 03:49:31,042] [INFO] Target genome list was writen to OceanDNA-b41392/target_genomes_gtdb.txt
[2023-03-15 03:49:31,058] [INFO] Task started: fastANI
[2023-03-15 03:49:31,058] [INFO] Running command: fastANI --query /var/lib/cwl/stge2859802-75c6-4a8a-81bf-c2f26933213d/OceanDNA-b41392.fa --refList OceanDNA-b41392/target_genomes_gtdb.txt --output OceanDNA-b41392/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:49:42,219] [INFO] Task succeeded: fastANI
[2023-03-15 03:49:42,228] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:49:42,228] [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_000967895.1	s__Oleispira antarctica	82.3806	772	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
GCA_002708475.1	s__Oleispira sp002708475	81.5999	388	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	98.91	98.91	0.78	0.78	2	-
GCA_002632185.1	s__Oleispira sp002632185	81.0037	363	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765295.1	s__Oleispira sp016765295	80.9655	375	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733645.1	s__Oleibacter sp002733645	77.1284	88	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	97.97	97.97	0.87	0.87	2	-
GCF_000355675.1	s__Thalassolituus oleivorans	77.0247	104	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCA_014859445.1	s__Bacterioplanes sp014859445	76.4984	64	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:49:42,228] [INFO] GTDB search result was written to OceanDNA-b41392/result_gtdb.tsv
[2023-03-15 03:49:42,228] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:49:42,230] [INFO] DFAST_QC result json was written to OceanDNA-b41392/dqc_result.json
[2023-03-15 03:49:42,230] [INFO] DFAST_QC completed!
[2023-03-15 03:49:42,230] [INFO] Total running time: 0h2m3s