[2023-03-15 17:09:05,940] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:09:05,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:09:05,941] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference
[2023-03-15 17:09:07,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:09:07,761] [INFO] Task started: Prodigal
[2023-03-15 17:09:07,762] [INFO] Running command: cat /var/lib/cwl/stg33ea27e2-410f-4f87-aac4-8c6a26d9176d/OceanDNA-b6564.fa | prodigal -d OceanDNA-b6564/cds.fna -a OceanDNA-b6564/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:09:30,673] [INFO] Task succeeded: Prodigal
[2023-03-15 17:09:30,673] [INFO] Task started: HMMsearch
[2023-03-15 17:09:30,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b6564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/reference_markers.hmm OceanDNA-b6564/protein.faa > /dev/null
[2023-03-15 17:09:30,873] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:09:30,873] [INFO] Found 6/6 markers.
[2023-03-15 17:09:30,897] [INFO] Query marker FASTA was written to OceanDNA-b6564/markers.fasta
[2023-03-15 17:09:30,898] [INFO] Task started: Blastn
[2023-03-15 17:09:30,898] [INFO] Running command: blastn -query OceanDNA-b6564/markers.fasta -db /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/reference_markers.fasta -out OceanDNA-b6564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:09:31,472] [INFO] Task succeeded: Blastn
[2023-03-15 17:09:31,475] [INFO] Selected 25 target genomes.
[2023-03-15 17:09:31,475] [INFO] Target genome list was writen to OceanDNA-b6564/target_genomes.txt
[2023-03-15 17:09:31,489] [INFO] Task started: fastANI
[2023-03-15 17:09:31,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg33ea27e2-410f-4f87-aac4-8c6a26d9176d/OceanDNA-b6564.fa --refList OceanDNA-b6564/target_genomes.txt --output OceanDNA-b6564/fastani_result.tsv --threads 1
[2023-03-15 17:09:46,106] [INFO] Task succeeded: fastANI
[2023-03-15 17:09:46,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:09:46,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:09:46,115] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:09:46,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:09:46,115] [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
Aureicoccus marinus	strain=SG-18	GCA_002954325.1	754435	754435	type	True	92.8964	843	971	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.4677	68	971	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.4401	69	971	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.2451	60	971	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.1818	59	971	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.1464	69	971	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.0908	51	971	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.0633	65	971	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.061	71	971	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	75.9639	54	971	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.9409	62	971	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	75.5964	50	971	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:09:46,116] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6564/tc_result.tsv
[2023-03-15 17:09:46,119] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:09:46,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:09:46,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/checkm_data
[2023-03-15 17:09:46,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:09:46,134] [INFO] Task started: CheckM
[2023-03-15 17:09:46,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6564/checkm_input OceanDNA-b6564/checkm_result
[2023-03-15 17:10:44,844] [INFO] Task succeeded: CheckM
[2023-03-15 17:10:44,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:10:44,865] [INFO] ===== Completeness check finished =====
[2023-03-15 17:10:44,865] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:10:44,865] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6564/markers.fasta)
[2023-03-15 17:10:44,867] [INFO] Task started: Blastn
[2023-03-15 17:10:44,867] [INFO] Running command: blastn -query OceanDNA-b6564/markers.fasta -db /var/lib/cwl/stgdbd5241e-5e32-4f43-910c-f85222de5bf6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:10:45,683] [INFO] Task succeeded: Blastn
[2023-03-15 17:10:45,690] [INFO] Selected 27 target genomes.
[2023-03-15 17:10:45,690] [INFO] Target genome list was writen to OceanDNA-b6564/target_genomes_gtdb.txt
[2023-03-15 17:10:45,736] [INFO] Task started: fastANI
[2023-03-15 17:10:45,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg33ea27e2-410f-4f87-aac4-8c6a26d9176d/OceanDNA-b6564.fa --refList OceanDNA-b6564/target_genomes_gtdb.txt --output OceanDNA-b6564/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:11:03,965] [INFO] Task succeeded: fastANI
[2023-03-15 17:11:03,973] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:11:03,973] [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_002954325.1	s__Aureicoccus marinus	92.8964	843	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.4625	67	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013911645.1	s__Muricauda sp013911645	76.4259	63	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	76.3411	71	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.2595	76	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_004804315.1	s__Muricauda sp004804315	76.2451	60	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.21	58	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	76.17	68	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	76.1479	67	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_009184425.1	s__Muricauda olearia	76.0938	68	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003058265.1	s__Muricauda sp003058265	76.0756	63	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	75.9638	61	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:11:03,974] [INFO] GTDB search result was written to OceanDNA-b6564/result_gtdb.tsv
[2023-03-15 17:11:03,977] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:11:03,983] [INFO] DFAST_QC result json was written to OceanDNA-b6564/dqc_result.json
[2023-03-15 17:11:03,983] [INFO] DFAST_QC completed!
[2023-03-15 17:11:03,983] [INFO] Total running time: 0h1m58s