[2023-03-15 07:29:11,758] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,759] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,590] [INFO] Running command: cat /var/lib/cwl/stg09e47a31-c92b-49ca-b67b-d413cc460555/OceanDNA-b34615.fa | prodigal -d OceanDNA-b34615/cds.fna -a OceanDNA-b34615/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:34,911] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:34,911] [INFO] Task started: HMMsearch
[2023-03-15 07:29:34,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b34615/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/reference_markers.hmm OceanDNA-b34615/protein.faa > /dev/null
[2023-03-15 07:29:35,146] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:35,146] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg09e47a31-c92b-49ca-b67b-d413cc460555/OceanDNA-b34615.fa]
[2023-03-15 07:29:35,178] [INFO] Query marker FASTA was written to OceanDNA-b34615/markers.fasta
[2023-03-15 07:29:35,180] [INFO] Task started: Blastn
[2023-03-15 07:29:35,180] [INFO] Running command: blastn -query OceanDNA-b34615/markers.fasta -db /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/reference_markers.fasta -out OceanDNA-b34615/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:35,827] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:35,828] [INFO] Selected 14 target genomes.
[2023-03-15 07:29:35,829] [INFO] Target genome list was writen to OceanDNA-b34615/target_genomes.txt
[2023-03-15 07:29:35,837] [INFO] Task started: fastANI
[2023-03-15 07:29:35,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e47a31-c92b-49ca-b67b-d413cc460555/OceanDNA-b34615.fa --refList OceanDNA-b34615/target_genomes.txt --output OceanDNA-b34615/fastani_result.tsv --threads 1
[2023-03-15 07:29:46,053] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:46,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:46,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:46,062] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 07:29:46,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 07:29:46,062] [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
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	95.8442	1072	1253	95	conclusive
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	86.1779	957	1253	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	82.527	871	1253	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	78.9558	406	1253	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.8773	397	1253	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.6952	419	1253	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.6828	385	1253	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.5619	432	1253	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	78.5183	290	1253	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	77.0613	171	1253	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	76.9889	166	1253	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	76.963	162	1253	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	76.9547	170	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:46,062] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34615/tc_result.tsv
[2023-03-15 07:29:46,062] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:46,063] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:46,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/checkm_data
[2023-03-15 07:29:46,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:46,076] [INFO] Task started: CheckM
[2023-03-15 07:29:46,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34615/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34615/checkm_input OceanDNA-b34615/checkm_result
[2023-03-15 07:30:39,153] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:39,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:39,156] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:39,156] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:39,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34615/markers.fasta)
[2023-03-15 07:30:39,158] [INFO] Task started: Blastn
[2023-03-15 07:30:39,158] [INFO] Running command: blastn -query OceanDNA-b34615/markers.fasta -db /var/lib/cwl/stg3f0ac8fc-fee2-4e83-95ae-6b6bfcbad51e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34615/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:39,958] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:39,959] [INFO] Selected 12 target genomes.
[2023-03-15 07:30:39,959] [INFO] Target genome list was writen to OceanDNA-b34615/target_genomes_gtdb.txt
[2023-03-15 07:30:39,967] [INFO] Task started: fastANI
[2023-03-15 07:30:39,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e47a31-c92b-49ca-b67b-d413cc460555/OceanDNA-b34615.fa --refList OceanDNA-b34615/target_genomes_gtdb.txt --output OceanDNA-b34615/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:49,064] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:49,070] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:49,071] [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_000382165.1	s__Arsukibacterium perlucidum	95.8314	1073	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900215315.1	s__Arsukibacterium tuosuense	86.1778	958	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	84.4269	910	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019100565.1	s__Arsukibacterium sp019100565	82.4996	874	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	82.3135	845	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415085.1	s__Arsukibacterium sp002415085	81.8793	811	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCA_002364615.1	s__Arsukibacterium sp002364615	81.6376	817	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCA_018826295.1	s__Rheinheimera sp018826295	78.5205	414	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_000245735.1	s__Alishewanella jeotgali	78.082	330	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_014645135.1	s__Pararheinheimera tangshanensis	76.9625	163	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.63	97.26	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:49,071] [INFO] GTDB search result was written to OceanDNA-b34615/result_gtdb.tsv
[2023-03-15 07:30:49,071] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:49,072] [INFO] DFAST_QC result json was written to OceanDNA-b34615/dqc_result.json
[2023-03-15 07:30:49,072] [INFO] DFAST_QC completed!
[2023-03-15 07:30:49,073] [INFO] Total running time: 0h1m37s