[2023-03-18 07:06:22,062] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,063] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference
[2023-03-18 07:06:23,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,194] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,195] [INFO] Running command: cat /var/lib/cwl/stg8bedd9c6-797d-40f3-9530-b9445129ddf8/OceanDNA-b32197.fa | prodigal -d OceanDNA-b32197/cds.fna -a OceanDNA-b32197/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:41,022] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:41,022] [INFO] Task started: HMMsearch
[2023-03-18 07:06:41,022] [INFO] Running command: hmmsearch --tblout OceanDNA-b32197/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/reference_markers.hmm OceanDNA-b32197/protein.faa > /dev/null
[2023-03-18 07:06:41,253] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:41,253] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8bedd9c6-797d-40f3-9530-b9445129ddf8/OceanDNA-b32197.fa]
[2023-03-18 07:06:41,274] [INFO] Query marker FASTA was written to OceanDNA-b32197/markers.fasta
[2023-03-18 07:06:41,275] [INFO] Task started: Blastn
[2023-03-18 07:06:41,275] [INFO] Running command: blastn -query OceanDNA-b32197/markers.fasta -db /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/reference_markers.fasta -out OceanDNA-b32197/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:41,978] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:41,978] [INFO] Selected 19 target genomes.
[2023-03-18 07:06:41,979] [INFO] Target genome list was writen to OceanDNA-b32197/target_genomes.txt
[2023-03-18 07:06:41,988] [INFO] Task started: fastANI
[2023-03-18 07:06:41,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bedd9c6-797d-40f3-9530-b9445129ddf8/OceanDNA-b32197.fa --refList OceanDNA-b32197/target_genomes.txt --output OceanDNA-b32197/fastani_result.tsv --threads 1
[2023-03-18 07:06:54,076] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:54,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:54,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:54,087] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:54,087] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:54,087] [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	84.0447	678	947	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.0034	305	947	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.8682	302	947	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.5135	253	947	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.4096	248	947	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	76.5831	118	947	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	76.5774	122	947	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.5727	116	947	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	76.5324	114	947	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.4752	131	947	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	76.4494	118	947	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.4303	106	947	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.3554	112	947	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.2563	111	947	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.2192	86	947	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	76.0239	93	947	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	75.9691	93	947	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	75.8866	71	947	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	75.8359	86	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:54,087] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32197/tc_result.tsv
[2023-03-18 07:06:54,087] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:54,087] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:54,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/checkm_data
[2023-03-18 07:06:54,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:54,092] [INFO] Task started: CheckM
[2023-03-18 07:06:54,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32197/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32197/checkm_input OceanDNA-b32197/checkm_result
[2023-03-18 07:07:39,778] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:39,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:39,781] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:39,781] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:39,781] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32197/markers.fasta)
[2023-03-18 07:07:39,782] [INFO] Task started: Blastn
[2023-03-18 07:07:39,782] [INFO] Running command: blastn -query OceanDNA-b32197/markers.fasta -db /var/lib/cwl/stga4c194aa-3532-4ccd-8452-3f7ba16b1d75/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32197/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:40,989] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:40,990] [INFO] Selected 11 target genomes.
[2023-03-18 07:07:40,990] [INFO] Target genome list was writen to OceanDNA-b32197/target_genomes_gtdb.txt
[2023-03-18 07:07:41,123] [INFO] Task started: fastANI
[2023-03-18 07:07:41,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bedd9c6-797d-40f3-9530-b9445129ddf8/OceanDNA-b32197.fa --refList OceanDNA-b32197/target_genomes_gtdb.txt --output OceanDNA-b32197/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:48,240] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:48,247] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:48,247] [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	84.0527	678	947	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	82.1294	585	947	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	82.0956	619	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	81.817	595	947	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	81.7651	499	947	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	81.4652	581	947	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	81.3665	599	947	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	81.3335	388	947	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	81.2484	463	947	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	80.4334	367	947	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	77.489	255	947	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 07:07:48,247] [INFO] GTDB search result was written to OceanDNA-b32197/result_gtdb.tsv
[2023-03-18 07:07:48,247] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:48,249] [INFO] DFAST_QC result json was written to OceanDNA-b32197/dqc_result.json
[2023-03-18 07:07:48,249] [INFO] DFAST_QC completed!
[2023-03-18 07:07:48,249] [INFO] Total running time: 0h1m26s