[2023-03-15 23:56:02,569] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,569] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference
[2023-03-15 23:56:03,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,655] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,655] [INFO] Running command: cat /var/lib/cwl/stg0769bff6-7f2a-4639-a6a9-ab5e8b179da6/OceanDNA-b32277.fa | prodigal -d OceanDNA-b32277/cds.fna -a OceanDNA-b32277/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:24,386] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:24,386] [INFO] Task started: HMMsearch
[2023-03-15 23:56:24,386] [INFO] Running command: hmmsearch --tblout OceanDNA-b32277/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/reference_markers.hmm OceanDNA-b32277/protein.faa > /dev/null
[2023-03-15 23:56:24,592] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:24,593] [INFO] Found 6/6 markers.
[2023-03-15 23:56:24,618] [INFO] Query marker FASTA was written to OceanDNA-b32277/markers.fasta
[2023-03-15 23:56:24,619] [INFO] Task started: Blastn
[2023-03-15 23:56:24,619] [INFO] Running command: blastn -query OceanDNA-b32277/markers.fasta -db /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/reference_markers.fasta -out OceanDNA-b32277/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:25,359] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:25,361] [INFO] Selected 17 target genomes.
[2023-03-15 23:56:25,362] [INFO] Target genome list was writen to OceanDNA-b32277/target_genomes.txt
[2023-03-15 23:56:25,407] [INFO] Task started: fastANI
[2023-03-15 23:56:25,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg0769bff6-7f2a-4639-a6a9-ab5e8b179da6/OceanDNA-b32277.fa --refList OceanDNA-b32277/target_genomes.txt --output OceanDNA-b32277/fastani_result.tsv --threads 1
[2023-03-15 23:56:36,787] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:36,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:36,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:36,797] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:36,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:56:36,798] [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	85.1338	787	1112	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.4709	379	1112	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.4387	384	1112	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.1915	341	1112	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0727	325	1112	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	77.165	147	1112	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.0812	191	1112	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	76.9458	167	1112	95	below_threshold
Novosphingopyxis iocasae	strain=PB63	GCA_014334095.1	2762729	2762729	type	True	76.9457	156	1112	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.9164	163	1112	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	76.8724	159	1112	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.8706	149	1112	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.8635	149	1112	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.8164	138	1112	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.8024	136	1112	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	76.7554	139	1112	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.3916	108	1112	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:56:36,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32277/tc_result.tsv
[2023-03-15 23:56:36,798] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:36,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:36,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/checkm_data
[2023-03-15 23:56:36,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:36,999] [INFO] Task started: CheckM
[2023-03-15 23:56:36,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32277/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32277/checkm_input OceanDNA-b32277/checkm_result
[2023-03-15 23:57:29,925] [INFO] Task succeeded: CheckM
[2023-03-15 23:57:29,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:57:29,929] [INFO] ===== Completeness check finished =====
[2023-03-15 23:57:29,929] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:57:29,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32277/markers.fasta)
[2023-03-15 23:57:29,930] [INFO] Task started: Blastn
[2023-03-15 23:57:29,930] [INFO] Running command: blastn -query OceanDNA-b32277/markers.fasta -db /var/lib/cwl/stgcb925a51-ab0c-4b9a-9f99-ebaa8b14ae68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32277/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:57:31,292] [INFO] Task succeeded: Blastn
[2023-03-15 23:57:31,293] [INFO] Selected 11 target genomes.
[2023-03-15 23:57:31,293] [INFO] Target genome list was writen to OceanDNA-b32277/target_genomes_gtdb.txt
[2023-03-15 23:57:31,386] [INFO] Task started: fastANI
[2023-03-15 23:57:31,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg0769bff6-7f2a-4639-a6a9-ab5e8b179da6/OceanDNA-b32277.fa --refList OceanDNA-b32277/target_genomes_gtdb.txt --output OceanDNA-b32277/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:57:39,134] [INFO] Task succeeded: fastANI
[2023-03-15 23:57:39,141] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:57:39,142] [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_013371215.1	s__Parasphingorhabdus flavimaris	85.1338	787	1112	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	84.8929	630	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	84.8064	819	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	84.6907	751	1112	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	83.5447	435	1112	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	83.3639	745	1112	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	83.1407	743	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	82.9253	714	1112	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	82.8748	567	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_013204445.1	s__Parasphingorhabdus sp013204445	82.3985	425	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498565.1	s__Parasphingorhabdus sp017498565	78.1915	341	1112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:57:39,142] [INFO] GTDB search result was written to OceanDNA-b32277/result_gtdb.tsv
[2023-03-15 23:57:39,142] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:57:39,144] [INFO] DFAST_QC result json was written to OceanDNA-b32277/dqc_result.json
[2023-03-15 23:57:39,144] [INFO] DFAST_QC completed!
[2023-03-15 23:57:39,144] [INFO] Total running time: 0h1m37s