[2023-03-16 04:05:20,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,127] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,128] [INFO] Running command: cat /var/lib/cwl/stg103dbfee-be53-4f29-8ba8-4fba9c69bbf7/OceanDNA-b24103.fa | prodigal -d OceanDNA-b24103/cds.fna -a OceanDNA-b24103/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:38,464] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:38,464] [INFO] Task started: HMMsearch
[2023-03-16 04:05:38,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b24103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/reference_markers.hmm OceanDNA-b24103/protein.faa > /dev/null
[2023-03-16 04:05:38,657] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:38,658] [INFO] Found 6/6 markers.
[2023-03-16 04:05:38,683] [INFO] Query marker FASTA was written to OceanDNA-b24103/markers.fasta
[2023-03-16 04:05:38,683] [INFO] Task started: Blastn
[2023-03-16 04:05:38,683] [INFO] Running command: blastn -query OceanDNA-b24103/markers.fasta -db /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/reference_markers.fasta -out OceanDNA-b24103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:39,286] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:39,287] [INFO] Selected 33 target genomes.
[2023-03-16 04:05:39,287] [INFO] Target genome list was writen to OceanDNA-b24103/target_genomes.txt
[2023-03-16 04:05:39,303] [INFO] Task started: fastANI
[2023-03-16 04:05:39,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg103dbfee-be53-4f29-8ba8-4fba9c69bbf7/OceanDNA-b24103.fa --refList OceanDNA-b24103/target_genomes.txt --output OceanDNA-b24103/fastani_result.tsv --threads 1
[2023-03-16 04:06:03,444] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:03,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:03,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:03,452] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:03,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:03,452] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.1668	67	866	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.8624	73	866	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.8602	64	866	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.8587	74	866	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.6972	70	866	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.6367	58	866	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.5751	60	866	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.4366	74	866	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	75.4077	50	866	95	below_threshold
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	75.0465	56	866	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.0396	50	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:03,452] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24103/tc_result.tsv
[2023-03-16 04:06:03,452] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:03,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:03,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/checkm_data
[2023-03-16 04:06:03,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:03,458] [INFO] Task started: CheckM
[2023-03-16 04:06:03,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24103/checkm_input OceanDNA-b24103/checkm_result
[2023-03-16 04:06:47,362] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:47,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:47,365] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:47,365] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:47,365] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24103/markers.fasta)
[2023-03-16 04:06:47,366] [INFO] Task started: Blastn
[2023-03-16 04:06:47,366] [INFO] Running command: blastn -query OceanDNA-b24103/markers.fasta -db /var/lib/cwl/stg39f4ee62-ea02-4b18-9f79-b2b4c0bb0f93/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:48,339] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:48,340] [INFO] Selected 33 target genomes.
[2023-03-16 04:06:48,340] [INFO] Target genome list was writen to OceanDNA-b24103/target_genomes_gtdb.txt
[2023-03-16 04:06:48,398] [INFO] Task started: fastANI
[2023-03-16 04:06:48,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg103dbfee-be53-4f29-8ba8-4fba9c69bbf7/OceanDNA-b24103.fa --refList OceanDNA-b24103/target_genomes_gtdb.txt --output OceanDNA-b24103/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:10,429] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:10,438] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:10,438] [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_905181725.1	s__UBA830 sp905181725	78.5292	349	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	77.9616	314	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002471575.1	s__UBA830 sp002471575	77.2404	207	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_002689465.1	s__UBA830 sp002689465	77.0898	69	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.2783	123	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.1668	67	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.1571	59	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_018660305.1	s__JABJKO01 sp018660305	75.9658	92	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_016869145.1	s__VGEU01 sp016869145	75.8989	117	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.828	53	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	75.7234	53	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	75.6972	70	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	75.6572	60	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCF_014904705.1	s__Nisaea sp014904705	75.6367	58	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	75.5711	60	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.4229	75	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:10,439] [INFO] GTDB search result was written to OceanDNA-b24103/result_gtdb.tsv
[2023-03-16 04:07:10,439] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:10,440] [INFO] DFAST_QC result json was written to OceanDNA-b24103/dqc_result.json
[2023-03-16 04:07:10,440] [INFO] DFAST_QC completed!
[2023-03-16 04:07:10,441] [INFO] Total running time: 0h1m50s