[2023-03-19 04:43:18,663] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference
[2023-03-19 04:43:19,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,798] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,798] [INFO] Running command: cat /var/lib/cwl/stg1553b485-818f-4142-a4e9-dbe768f4e665/OceanDNA-b26716.fa | prodigal -d OceanDNA-b26716/cds.fna -a OceanDNA-b26716/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:40,927] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:40,927] [INFO] Task started: HMMsearch
[2023-03-19 04:43:40,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b26716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/reference_markers.hmm OceanDNA-b26716/protein.faa > /dev/null
[2023-03-19 04:43:41,121] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:41,122] [INFO] Found 6/6 markers.
[2023-03-19 04:43:41,142] [INFO] Query marker FASTA was written to OceanDNA-b26716/markers.fasta
[2023-03-19 04:43:41,142] [INFO] Task started: Blastn
[2023-03-19 04:43:41,142] [INFO] Running command: blastn -query OceanDNA-b26716/markers.fasta -db /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/reference_markers.fasta -out OceanDNA-b26716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:41,953] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:41,954] [INFO] Selected 12 target genomes.
[2023-03-19 04:43:41,954] [INFO] Target genome list was writen to OceanDNA-b26716/target_genomes.txt
[2023-03-19 04:43:41,961] [INFO] Task started: fastANI
[2023-03-19 04:43:41,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg1553b485-818f-4142-a4e9-dbe768f4e665/OceanDNA-b26716.fa --refList OceanDNA-b26716/target_genomes.txt --output OceanDNA-b26716/fastani_result.tsv --threads 1
[2023-03-19 04:43:50,632] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:50,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:50,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:50,641] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:50,641] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:50,641] [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	87.7032	917	1098	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	80.772	542	1098	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	80.6964	587	1098	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.5277	470	1098	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	78.8105	408	1098	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.7898	452	1098	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.6981	433	1098	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.5635	376	1098	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	77.5855	255	1098	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.4775	258	1098	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.3554	323	1098	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.8689	118	1098	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:50,641] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26716/tc_result.tsv
[2023-03-19 04:43:50,642] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:50,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:50,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/checkm_data
[2023-03-19 04:43:50,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:50,651] [INFO] Task started: CheckM
[2023-03-19 04:43:50,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26716/checkm_input OceanDNA-b26716/checkm_result
[2023-03-19 04:44:43,346] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:43,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:43,349] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:43,349] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:43,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26716/markers.fasta)
[2023-03-19 04:44:43,350] [INFO] Task started: Blastn
[2023-03-19 04:44:43,350] [INFO] Running command: blastn -query OceanDNA-b26716/markers.fasta -db /var/lib/cwl/stgb2aab385-f3ae-417e-91d6-cd64edf1f60d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:44,888] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:44,889] [INFO] Selected 7 target genomes.
[2023-03-19 04:44:44,889] [INFO] Target genome list was writen to OceanDNA-b26716/target_genomes_gtdb.txt
[2023-03-19 04:44:44,911] [INFO] Task started: fastANI
[2023-03-19 04:44:44,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg1553b485-818f-4142-a4e9-dbe768f4e665/OceanDNA-b26716.fa --refList OceanDNA-b26716/target_genomes_gtdb.txt --output OceanDNA-b26716/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:50,634] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:50,639] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:44:50,640] [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_002723255.1	s__Pelagibacterium sp002723255	99.6579	909	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	conclusive
GCA_002375765.1	s__Pelagibacterium sp002375765	87.758	863	1098	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	87.7032	917	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002337455.1	s__Pelagibacterium sp002337455	86.5461	868	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_003345525.1	s__Pelagibacterium lacus	80.7493	544	1098	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	80.6821	588	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758415.1	s__Devosia marina	77.5883	254	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:50,640] [INFO] GTDB search result was written to OceanDNA-b26716/result_gtdb.tsv
[2023-03-19 04:44:50,640] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:50,641] [INFO] DFAST_QC result json was written to OceanDNA-b26716/dqc_result.json
[2023-03-19 04:44:50,641] [INFO] DFAST_QC completed!
[2023-03-19 04:44:50,641] [INFO] Total running time: 0h1m32s