[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference
[2023-03-14 11:14:14,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,241] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,241] [INFO] Running command: cat /var/lib/cwl/stgbb8ef4e0-f12c-4176-bb8f-f81577c25fbe/OceanDNA-b26703.fa | prodigal -d OceanDNA-b26703/cds.fna -a OceanDNA-b26703/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:38,664] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:38,665] [INFO] Task started: HMMsearch
[2023-03-14 11:14:38,665] [INFO] Running command: hmmsearch --tblout OceanDNA-b26703/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/reference_markers.hmm OceanDNA-b26703/protein.faa > /dev/null
[2023-03-14 11:14:38,934] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:38,935] [INFO] Found 6/6 markers.
[2023-03-14 11:14:38,973] [INFO] Query marker FASTA was written to OceanDNA-b26703/markers.fasta
[2023-03-14 11:14:38,975] [INFO] Task started: Blastn
[2023-03-14 11:14:38,975] [INFO] Running command: blastn -query OceanDNA-b26703/markers.fasta -db /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/reference_markers.fasta -out OceanDNA-b26703/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:39,839] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:39,840] [INFO] Selected 14 target genomes.
[2023-03-14 11:14:39,840] [INFO] Target genome list was writen to OceanDNA-b26703/target_genomes.txt
[2023-03-14 11:14:39,852] [INFO] Task started: fastANI
[2023-03-14 11:14:39,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8ef4e0-f12c-4176-bb8f-f81577c25fbe/OceanDNA-b26703.fa --refList OceanDNA-b26703/target_genomes.txt --output OceanDNA-b26703/fastani_result.tsv --threads 1
[2023-03-14 11:14:50,608] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:50,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:50,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:50,618] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:50,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:50,618] [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
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	85.9247	912	1259	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	80.5051	545	1259	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	80.337	584	1259	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.3024	476	1259	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.5457	433	1259	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	78.541	391	1259	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.4748	393	1259	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.3819	369	1259	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.6325	276	1259	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	77.4988	277	1259	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	77.4373	259	1259	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	77.3947	234	1259	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	76.6287	145	1259	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.5477	108	1259	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:50,618] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26703/tc_result.tsv
[2023-03-14 11:14:50,618] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:50,619] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:50,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/checkm_data
[2023-03-14 11:14:50,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:50,661] [INFO] Task started: CheckM
[2023-03-14 11:14:50,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26703/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26703/checkm_input OceanDNA-b26703/checkm_result
[2023-03-14 11:15:49,768] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:49,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:49,772] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:49,772] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:49,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26703/markers.fasta)
[2023-03-14 11:15:49,773] [INFO] Task started: Blastn
[2023-03-14 11:15:49,773] [INFO] Running command: blastn -query OceanDNA-b26703/markers.fasta -db /var/lib/cwl/stgc5f80db7-70b2-4d69-aa7c-462b707c7dd9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26703/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:51,257] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:51,258] [INFO] Selected 10 target genomes.
[2023-03-14 11:15:51,258] [INFO] Target genome list was writen to OceanDNA-b26703/target_genomes_gtdb.txt
[2023-03-14 11:15:51,270] [INFO] Task started: fastANI
[2023-03-14 11:15:51,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8ef4e0-f12c-4176-bb8f-f81577c25fbe/OceanDNA-b26703.fa --refList OceanDNA-b26703/target_genomes_gtdb.txt --output OceanDNA-b26703/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:59,325] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:59,332] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:59,332] [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_002337455.1	s__Pelagibacterium sp002337455	99.9837	1198	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	conclusive
GCA_002723255.1	s__Pelagibacterium sp002723255	86.4766	756	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	86.2274	897	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_000230555.1	s__Pelagibacterium halotolerans	85.9247	912	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_003345525.1	s__Pelagibacterium lacus	80.4943	546	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	80.3488	584	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	79.3072	476	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992665.1	s__Pelagibacterium montanilacus	78.4454	393	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	77.4148	288	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735585.1	s__Devosia sp000735585	77.3824	268	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:59,332] [INFO] GTDB search result was written to OceanDNA-b26703/result_gtdb.tsv
[2023-03-14 11:15:59,332] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:59,334] [INFO] DFAST_QC result json was written to OceanDNA-b26703/dqc_result.json
[2023-03-14 11:15:59,334] [INFO] DFAST_QC completed!
[2023-03-14 11:15:59,334] [INFO] Total running time: 0h1m47s