[2023-03-16 08:20:04,380] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:20:04,381] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:20:04,381] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference
[2023-03-16 08:20:05,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:20:05,529] [INFO] Task started: Prodigal
[2023-03-16 08:20:05,529] [INFO] Running command: cat /var/lib/cwl/stgc26020bf-511c-4326-b744-0ce5da0d65f7/OceanDNA-b29503.fa | prodigal -d OceanDNA-b29503/cds.fna -a OceanDNA-b29503/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:20:39,125] [INFO] Task succeeded: Prodigal
[2023-03-16 08:20:39,125] [INFO] Task started: HMMsearch
[2023-03-16 08:20:39,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b29503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/reference_markers.hmm OceanDNA-b29503/protein.faa > /dev/null
[2023-03-16 08:20:39,359] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:20:39,359] [INFO] Found 6/6 markers.
[2023-03-16 08:20:39,390] [INFO] Query marker FASTA was written to OceanDNA-b29503/markers.fasta
[2023-03-16 08:20:39,391] [INFO] Task started: Blastn
[2023-03-16 08:20:39,391] [INFO] Running command: blastn -query OceanDNA-b29503/markers.fasta -db /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/reference_markers.fasta -out OceanDNA-b29503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:20:40,192] [INFO] Task succeeded: Blastn
[2023-03-16 08:20:40,196] [INFO] Selected 20 target genomes.
[2023-03-16 08:20:40,196] [INFO] Target genome list was writen to OceanDNA-b29503/target_genomes.txt
[2023-03-16 08:20:40,218] [INFO] Task started: fastANI
[2023-03-16 08:20:40,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26020bf-511c-4326-b744-0ce5da0d65f7/OceanDNA-b29503.fa --refList OceanDNA-b29503/target_genomes.txt --output OceanDNA-b29503/fastani_result.tsv --threads 1
[2023-03-16 08:20:58,805] [INFO] Task succeeded: fastANI
[2023-03-16 08:20:58,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:20:58,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:20:58,817] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:20:58,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:20:58,817] [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
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	90.3956	1432	1694	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	90.3785	1439	1694	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	82.5336	1118	1694	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.4694	714	1694	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.2471	672	1694	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.2412	717	1694	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.1799	687	1694	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.0666	680	1694	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.6569	549	1694	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6545	598	1694	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	78.6263	542	1694	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.6056	552	1694	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.5595	527	1694	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.5386	557	1694	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.3178	507	1694	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.2527	468	1694	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1017	500	1694	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.7285	398	1694	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	77.6947	375	1694	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0527	305	1694	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:20:58,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29503/tc_result.tsv
[2023-03-16 08:20:58,820] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:20:58,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:20:58,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/checkm_data
[2023-03-16 08:20:58,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:20:58,828] [INFO] Task started: CheckM
[2023-03-16 08:20:58,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29503/checkm_input OceanDNA-b29503/checkm_result
[2023-03-16 08:22:25,549] [INFO] Task succeeded: CheckM
[2023-03-16 08:22:25,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:22:25,565] [INFO] ===== Completeness check finished =====
[2023-03-16 08:22:25,565] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:22:25,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29503/markers.fasta)
[2023-03-16 08:22:25,567] [INFO] Task started: Blastn
[2023-03-16 08:22:25,567] [INFO] Running command: blastn -query OceanDNA-b29503/markers.fasta -db /var/lib/cwl/stgf1b33610-901c-49e6-9364-bb82fafdcac0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:27,070] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:27,073] [INFO] Selected 16 target genomes.
[2023-03-16 08:22:27,073] [INFO] Target genome list was writen to OceanDNA-b29503/target_genomes_gtdb.txt
[2023-03-16 08:22:27,091] [INFO] Task started: fastANI
[2023-03-16 08:22:27,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26020bf-511c-4326-b744-0ce5da0d65f7/OceanDNA-b29503.fa --refList OceanDNA-b29503/target_genomes_gtdb.txt --output OceanDNA-b29503/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:22:45,009] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:45,018] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:22:45,018] [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_900101505.1	s__Mameliella alba	90.3956	1432	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_019218285.1	s__DP3N28-2 sp019218285	82.5483	1116	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	82.4672	1088	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	81.722	1045	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	80.9557	1006	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.7882	894	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	80.7147	876	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	80.6056	859	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002814095.1	s__Sagittula sp002814095	80.1506	882	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	80.0972	812	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	80.0699	841	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	79.8507	793	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	79.4868	711	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900107235.1	s__Citreimonas salinaria	79.3734	633	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	79.2669	713	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_009363255.1	s__Roseivivax sp009363255	78.4325	489	1694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:22:45,020] [INFO] GTDB search result was written to OceanDNA-b29503/result_gtdb.tsv
[2023-03-16 08:22:45,022] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:22:45,026] [INFO] DFAST_QC result json was written to OceanDNA-b29503/dqc_result.json
[2023-03-16 08:22:45,026] [INFO] DFAST_QC completed!
[2023-03-16 08:22:45,026] [INFO] Total running time: 0h2m41s