[2023-03-15 05:51:32,069] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stg4cbac232-de5a-4dfd-9dd6-ad55ca03e2d7/OceanDNA-b32284.fa | prodigal -d OceanDNA-b32284/cds.fna -a OceanDNA-b32284/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:51,651] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:51,652] [INFO] Task started: HMMsearch
[2023-03-15 05:51:51,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b32284/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/reference_markers.hmm OceanDNA-b32284/protein.faa > /dev/null
[2023-03-15 05:51:51,853] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:51,854] [INFO] Found 6/6 markers.
[2023-03-15 05:51:51,875] [INFO] Query marker FASTA was written to OceanDNA-b32284/markers.fasta
[2023-03-15 05:51:51,876] [INFO] Task started: Blastn
[2023-03-15 05:51:51,876] [INFO] Running command: blastn -query OceanDNA-b32284/markers.fasta -db /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/reference_markers.fasta -out OceanDNA-b32284/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:52,565] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:52,566] [INFO] Selected 16 target genomes.
[2023-03-15 05:51:52,566] [INFO] Target genome list was writen to OceanDNA-b32284/target_genomes.txt
[2023-03-15 05:51:52,576] [INFO] Task started: fastANI
[2023-03-15 05:51:52,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbac232-de5a-4dfd-9dd6-ad55ca03e2d7/OceanDNA-b32284.fa --refList OceanDNA-b32284/target_genomes.txt --output OceanDNA-b32284/fastani_result.tsv --threads 1
[2023-03-15 05:52:03,681] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:03,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:03,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:03,691] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:03,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:52:03,692] [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	83.4143	701	964	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.0128	324	964	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	77.6253	313	964	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.5653	283	964	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.5266	256	964	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.5252	98	964	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	76.3913	106	964	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.308	110	964	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.2941	97	964	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.2518	107	964	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	76.2501	113	964	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.2236	122	964	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.109	109	964	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	76.0941	98	964	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.0625	109	964	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	75.9118	109	964	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:03,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32284/tc_result.tsv
[2023-03-15 05:52:03,694] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:03,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:03,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/checkm_data
[2023-03-15 05:52:03,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:03,700] [INFO] Task started: CheckM
[2023-03-15 05:52:03,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32284/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32284/checkm_input OceanDNA-b32284/checkm_result
[2023-03-15 05:52:50,228] [INFO] Task succeeded: CheckM
[2023-03-15 05:52:50,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:52:50,244] [INFO] ===== Completeness check finished =====
[2023-03-15 05:52:50,244] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:52:50,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32284/markers.fasta)
[2023-03-15 05:52:50,245] [INFO] Task started: Blastn
[2023-03-15 05:52:50,246] [INFO] Running command: blastn -query OceanDNA-b32284/markers.fasta -db /var/lib/cwl/stg025d9255-86aa-4c66-9104-5a5e2529505b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32284/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:52:51,513] [INFO] Task succeeded: Blastn
[2023-03-15 05:52:51,517] [INFO] Selected 12 target genomes.
[2023-03-15 05:52:51,517] [INFO] Target genome list was writen to OceanDNA-b32284/target_genomes_gtdb.txt
[2023-03-15 05:52:51,528] [INFO] Task started: fastANI
[2023-03-15 05:52:51,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbac232-de5a-4dfd-9dd6-ad55ca03e2d7/OceanDNA-b32284.fa --refList OceanDNA-b32284/target_genomes_gtdb.txt --output OceanDNA-b32284/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:52:59,599] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:59,607] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:52:59,607] [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_001586275.1	s__Parasphingorhabdus sp001586275	84.3755	713	964	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	84.1397	576	964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204445.1	s__Parasphingorhabdus sp013204445	83.8113	432	964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	83.4239	700	964	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	83.3123	439	964	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	82.9308	682	964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	82.8789	530	964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	82.3121	678	964	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	82.0998	631	964	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	82.0531	629	964	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258045.1	s__Parasphingorhabdus sp900258045	77.8098	303	964	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	77.5561	283	964	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 05:52:59,610] [INFO] GTDB search result was written to OceanDNA-b32284/result_gtdb.tsv
[2023-03-15 05:52:59,612] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:52:59,614] [INFO] DFAST_QC result json was written to OceanDNA-b32284/dqc_result.json
[2023-03-15 05:52:59,615] [INFO] DFAST_QC completed!
[2023-03-15 05:52:59,615] [INFO] Total running time: 0h1m28s