[2023-03-14 10:55:58,931] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,942] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,942] [INFO] DQC Reference Directory: /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference
[2023-03-14 10:56:00,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,681] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,681] [INFO] Running command: cat /var/lib/cwl/stg07a91560-3586-4d66-99ba-22a564783f98/OceanDNA-b34671.fa | prodigal -d OceanDNA-b34671/cds.fna -a OceanDNA-b34671/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:21,882] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:21,883] [INFO] Task started: HMMsearch
[2023-03-14 10:56:21,883] [INFO] Running command: hmmsearch --tblout OceanDNA-b34671/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/reference_markers.hmm OceanDNA-b34671/protein.faa > /dev/null
[2023-03-14 10:56:22,251] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:22,252] [INFO] Found 6/6 markers.
[2023-03-14 10:56:22,276] [INFO] Query marker FASTA was written to OceanDNA-b34671/markers.fasta
[2023-03-14 10:56:22,276] [INFO] Task started: Blastn
[2023-03-14 10:56:22,276] [INFO] Running command: blastn -query OceanDNA-b34671/markers.fasta -db /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/reference_markers.fasta -out OceanDNA-b34671/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:22,959] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:22,960] [INFO] Selected 20 target genomes.
[2023-03-14 10:56:22,961] [INFO] Target genome list was writen to OceanDNA-b34671/target_genomes.txt
[2023-03-14 10:56:22,972] [INFO] Task started: fastANI
[2023-03-14 10:56:22,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a91560-3586-4d66-99ba-22a564783f98/OceanDNA-b34671.fa --refList OceanDNA-b34671/target_genomes.txt --output OceanDNA-b34671/fastani_result.tsv --threads 1
[2023-03-14 10:56:40,277] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:40,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:40,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:40,285] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:40,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:40,285] [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
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.3104	404	1328	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.7514	346	1328	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.6737	314	1328	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.5344	329	1328	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.2256	302	1328	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.2233	283	1328	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.0343	301	1328	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.9907	289	1328	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	76.1863	76	1328	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.0422	60	1328	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:40,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34671/tc_result.tsv
[2023-03-14 10:56:40,392] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:40,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:40,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/checkm_data
[2023-03-14 10:56:40,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:40,456] [INFO] Task started: CheckM
[2023-03-14 10:56:40,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34671/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34671/checkm_input OceanDNA-b34671/checkm_result
[2023-03-14 10:57:33,113] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:33,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:33,117] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:33,117] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:33,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34671/markers.fasta)
[2023-03-14 10:57:33,117] [INFO] Task started: Blastn
[2023-03-14 10:57:33,117] [INFO] Running command: blastn -query OceanDNA-b34671/markers.fasta -db /var/lib/cwl/stgf527b71f-02c0-4b2e-b4c7-87f2681a5d71/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34671/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:34,137] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:34,138] [INFO] Selected 12 target genomes.
[2023-03-14 10:57:34,138] [INFO] Target genome list was writen to OceanDNA-b34671/target_genomes_gtdb.txt
[2023-03-14 10:57:34,150] [INFO] Task started: fastANI
[2023-03-14 10:57:34,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a91560-3586-4d66-99ba-22a564783f98/OceanDNA-b34671.fa --refList OceanDNA-b34671/target_genomes_gtdb.txt --output OceanDNA-b34671/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:43,387] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:43,395] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:57:43,395] [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_016745015.1	s__Colwellia sp016745015	82.6468	574	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	80.4305	630	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	80.2928	583	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	80.0906	552	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	80.086	556	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	79.8665	440	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	79.8217	515	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	79.7888	555	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	79.7714	389	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	79.2931	404	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	79.1514	403	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_005885605.1	s__Colwellia ponticola	78.7409	348	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:43,395] [INFO] GTDB search result was written to OceanDNA-b34671/result_gtdb.tsv
[2023-03-14 10:57:43,395] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:43,397] [INFO] DFAST_QC result json was written to OceanDNA-b34671/dqc_result.json
[2023-03-14 10:57:43,397] [INFO] DFAST_QC completed!
[2023-03-14 10:57:43,397] [INFO] Total running time: 0h1m44s