[2023-03-18 20:59:43,926] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,686] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,686] [INFO] Running command: cat /var/lib/cwl/stg34265c71-fc76-4bb1-9adb-88dfa6653491/OceanDNA-b32200.fa | prodigal -d OceanDNA-b32200/cds.fna -a OceanDNA-b32200/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:08,243] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:08,244] [INFO] Task started: HMMsearch
[2023-03-18 21:00:08,244] [INFO] Running command: hmmsearch --tblout OceanDNA-b32200/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/reference_markers.hmm OceanDNA-b32200/protein.faa > /dev/null
[2023-03-18 21:00:08,492] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:08,493] [INFO] Found 6/6 markers.
[2023-03-18 21:00:08,515] [INFO] Query marker FASTA was written to OceanDNA-b32200/markers.fasta
[2023-03-18 21:00:08,515] [INFO] Task started: Blastn
[2023-03-18 21:00:08,515] [INFO] Running command: blastn -query OceanDNA-b32200/markers.fasta -db /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/reference_markers.fasta -out OceanDNA-b32200/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:09,345] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:09,346] [INFO] Selected 18 target genomes.
[2023-03-18 21:00:09,346] [INFO] Target genome list was writen to OceanDNA-b32200/target_genomes.txt
[2023-03-18 21:00:09,357] [INFO] Task started: fastANI
[2023-03-18 21:00:09,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg34265c71-fc76-4bb1-9adb-88dfa6653491/OceanDNA-b32200.fa --refList OceanDNA-b32200/target_genomes.txt --output OceanDNA-b32200/fastani_result.tsv --threads 1
[2023-03-18 21:00:21,860] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:21,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:21,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:21,872] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:21,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:21,872] [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
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	83.6532	744	1205	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.738	427	1205	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.1975	345	1205	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.1007	324	1205	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0947	303	1205	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	77.7514	218	1205	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.6251	289	1205	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	77.5431	224	1205	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.3765	208	1205	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.3242	195	1205	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	77.3055	232	1205	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.245	214	1205	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.1866	198	1205	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	77.1442	224	1205	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.0465	232	1205	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	76.977	176	1205	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.976	177	1205	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	76.7052	142	1205	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:21,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32200/tc_result.tsv
[2023-03-18 21:00:21,873] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:21,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:21,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/checkm_data
[2023-03-18 21:00:21,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:21,879] [INFO] Task started: CheckM
[2023-03-18 21:00:21,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32200/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32200/checkm_input OceanDNA-b32200/checkm_result
[2023-03-18 21:01:17,838] [INFO] Task succeeded: CheckM
[2023-03-18 21:01:17,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:01:17,852] [INFO] ===== Completeness check finished =====
[2023-03-18 21:01:17,852] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:01:17,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32200/markers.fasta)
[2023-03-18 21:01:17,853] [INFO] Task started: Blastn
[2023-03-18 21:01:17,853] [INFO] Running command: blastn -query OceanDNA-b32200/markers.fasta -db /var/lib/cwl/stgc0f29e00-280e-4e95-85f6-503b5adff8b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32200/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:01:19,512] [INFO] Task succeeded: Blastn
[2023-03-18 21:01:19,521] [INFO] Selected 10 target genomes.
[2023-03-18 21:01:19,521] [INFO] Target genome list was writen to OceanDNA-b32200/target_genomes_gtdb.txt
[2023-03-18 21:01:19,575] [INFO] Task started: fastANI
[2023-03-18 21:01:19,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg34265c71-fc76-4bb1-9adb-88dfa6653491/OceanDNA-b32200.fa --refList OceanDNA-b32200/target_genomes_gtdb.txt --output OceanDNA-b32200/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:27,273] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:27,280] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:27,280] [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_002354635.1	s__Parasphingorhabdus sp002354635	85.3593	812	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	85.2801	829	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	84.3206	494	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	84.1463	628	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	83.8128	833	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	83.6532	744	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	83.0957	747	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	83.0339	745	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	82.9314	784	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479715.1	s__Parasphingorhabdus sp905479715	82.6033	587	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:27,286] [INFO] GTDB search result was written to OceanDNA-b32200/result_gtdb.tsv
[2023-03-18 21:01:27,288] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:27,295] [INFO] DFAST_QC result json was written to OceanDNA-b32200/dqc_result.json
[2023-03-18 21:01:27,295] [INFO] DFAST_QC completed!
[2023-03-18 21:01:27,295] [INFO] Total running time: 0h1m43s