[2023-03-17 11:52:51,138] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:52:51,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:52:51,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference
[2023-03-17 11:52:52,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:52:52,828] [INFO] Task started: Prodigal
[2023-03-17 11:52:52,828] [INFO] Running command: cat /var/lib/cwl/stgd992c2ce-ba8e-4d73-a4f0-e8a32869bf81/OceanDNA-b23314.fa | prodigal -d OceanDNA-b23314/cds.fna -a OceanDNA-b23314/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:53:06,517] [INFO] Task succeeded: Prodigal
[2023-03-17 11:53:06,518] [INFO] Task started: HMMsearch
[2023-03-17 11:53:06,518] [INFO] Running command: hmmsearch --tblout OceanDNA-b23314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/reference_markers.hmm OceanDNA-b23314/protein.faa > /dev/null
[2023-03-17 11:53:06,707] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:53:06,708] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd992c2ce-ba8e-4d73-a4f0-e8a32869bf81/OceanDNA-b23314.fa]
[2023-03-17 11:53:06,776] [INFO] Query marker FASTA was written to OceanDNA-b23314/markers.fasta
[2023-03-17 11:53:06,777] [INFO] Task started: Blastn
[2023-03-17 11:53:06,777] [INFO] Running command: blastn -query OceanDNA-b23314/markers.fasta -db /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/reference_markers.fasta -out OceanDNA-b23314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:07,391] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:07,413] [INFO] Selected 17 target genomes.
[2023-03-17 11:53:07,414] [INFO] Target genome list was writen to OceanDNA-b23314/target_genomes.txt
[2023-03-17 11:53:07,423] [INFO] Task started: fastANI
[2023-03-17 11:53:07,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgd992c2ce-ba8e-4d73-a4f0-e8a32869bf81/OceanDNA-b23314.fa --refList OceanDNA-b23314/target_genomes.txt --output OceanDNA-b23314/fastani_result.tsv --threads 1
[2023-03-17 11:53:22,201] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:22,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:53:22,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:53:22,212] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:53:22,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:53:22,212] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.421	127	564	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3291	162	564	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2983	161	564	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2867	133	564	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.1908	123	564	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.078	133	564	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.9686	131	564	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.7444	94	564	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.7428	74	564	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	75.68	90	564	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	75.6735	84	564	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.457	92	564	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.4345	105	564	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.1545	50	564	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:53:22,215] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23314/tc_result.tsv
[2023-03-17 11:53:22,221] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:53:22,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:53:22,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/checkm_data
[2023-03-17 11:53:22,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:53:22,319] [INFO] Task started: CheckM
[2023-03-17 11:53:22,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23314/checkm_input OceanDNA-b23314/checkm_result
[2023-03-17 11:53:59,479] [INFO] Task succeeded: CheckM
[2023-03-17 11:53:59,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:53:59,640] [INFO] ===== Completeness check finished =====
[2023-03-17 11:53:59,640] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:53:59,640] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23314/markers.fasta)
[2023-03-17 11:53:59,642] [INFO] Task started: Blastn
[2023-03-17 11:53:59,642] [INFO] Running command: blastn -query OceanDNA-b23314/markers.fasta -db /var/lib/cwl/stgebcbc612-92ff-45b4-83ee-3184c9750f8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:54:00,603] [INFO] Task succeeded: Blastn
[2023-03-17 11:54:00,611] [INFO] Selected 18 target genomes.
[2023-03-17 11:54:00,611] [INFO] Target genome list was writen to OceanDNA-b23314/target_genomes_gtdb.txt
[2023-03-17 11:54:00,647] [INFO] Task started: fastANI
[2023-03-17 11:54:00,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgd992c2ce-ba8e-4d73-a4f0-e8a32869bf81/OceanDNA-b23314.fa --refList OceanDNA-b23314/target_genomes_gtdb.txt --output OceanDNA-b23314/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:54:14,363] [INFO] Task succeeded: fastANI
[2023-03-17 11:54:14,371] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:54:14,371] [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_008039615.1	s__SYSU-D60007 sp008039615	76.376	130	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.3175	163	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017876095.1	s__Azospirillum agricola	76.3011	132	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_009377445.1	s__WHUA01 sp009377445	76.2681	90	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969625.1	s__Algihabitans sp006969625	76.1959	99	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	76.1125	119	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016869645.1	s__SHVW01 sp016869645	75.9792	75	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	75.8706	97	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355985.1	s__Desertibacter sp017355985	75.7588	93	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	75.7368	63	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	75.5541	87	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	75.5323	53	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCF_016653355.1	s__Rhodoplanes elegans	75.4345	105	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:54:14,380] [INFO] GTDB search result was written to OceanDNA-b23314/result_gtdb.tsv
[2023-03-17 11:54:14,394] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:54:14,404] [INFO] DFAST_QC result json was written to OceanDNA-b23314/dqc_result.json
[2023-03-17 11:54:14,404] [INFO] DFAST_QC completed!
[2023-03-17 11:54:14,404] [INFO] Total running time: 0h1m23s