[2023-03-16 04:05:20,416] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,416] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference
[2023-03-16 04:05:22,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stg6972dfc8-f730-44ff-9ecb-a9f3eeb8806c/OceanDNA-b34304.fa | prodigal -d OceanDNA-b34304/cds.fna -a OceanDNA-b34304/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:35,019] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:35,019] [INFO] Task started: HMMsearch
[2023-03-16 04:05:35,019] [INFO] Running command: hmmsearch --tblout OceanDNA-b34304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/reference_markers.hmm OceanDNA-b34304/protein.faa > /dev/null
[2023-03-16 04:05:35,225] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:35,226] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6972dfc8-f730-44ff-9ecb-a9f3eeb8806c/OceanDNA-b34304.fa]
[2023-03-16 04:05:35,249] [INFO] Query marker FASTA was written to OceanDNA-b34304/markers.fasta
[2023-03-16 04:05:35,250] [INFO] Task started: Blastn
[2023-03-16 04:05:35,250] [INFO] Running command: blastn -query OceanDNA-b34304/markers.fasta -db /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/reference_markers.fasta -out OceanDNA-b34304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:35,827] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:35,827] [INFO] Selected 14 target genomes.
[2023-03-16 04:05:35,828] [INFO] Target genome list was writen to OceanDNA-b34304/target_genomes.txt
[2023-03-16 04:05:35,836] [INFO] Task started: fastANI
[2023-03-16 04:05:35,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg6972dfc8-f730-44ff-9ecb-a9f3eeb8806c/OceanDNA-b34304.fa --refList OceanDNA-b34304/target_genomes.txt --output OceanDNA-b34304/fastani_result.tsv --threads 1
[2023-03-16 04:05:46,034] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:46,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:46,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:46,042] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:46,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:46,042] [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
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.758	328	680	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	79.7489	284	680	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.6995	335	680	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	79.4466	313	680	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.3237	302	680	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.8472	177	680	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.7107	193	680	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.6987	157	680	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.3908	181	680	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:46,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34304/tc_result.tsv
[2023-03-16 04:05:46,042] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:46,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:46,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/checkm_data
[2023-03-16 04:05:46,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:46,048] [INFO] Task started: CheckM
[2023-03-16 04:05:46,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34304/checkm_input OceanDNA-b34304/checkm_result
[2023-03-16 04:06:21,961] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:21,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.21%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:21,964] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:21,964] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:21,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34304/markers.fasta)
[2023-03-16 04:06:21,964] [INFO] Task started: Blastn
[2023-03-16 04:06:21,964] [INFO] Running command: blastn -query OceanDNA-b34304/markers.fasta -db /var/lib/cwl/stgceb7818a-b068-4ea6-bae9-5e1dcf0632da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:22,804] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:22,805] [INFO] Selected 14 target genomes.
[2023-03-16 04:06:22,805] [INFO] Target genome list was writen to OceanDNA-b34304/target_genomes_gtdb.txt
[2023-03-16 04:06:22,816] [INFO] Task started: fastANI
[2023-03-16 04:06:22,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg6972dfc8-f730-44ff-9ecb-a9f3eeb8806c/OceanDNA-b34304.fa --refList OceanDNA-b34304/target_genomes_gtdb.txt --output OceanDNA-b34304/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:32,601] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:32,610] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:06:32,610] [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_016756315.1	s__Alteromonas sp009811495	98.3737	675	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	conclusive
GCF_001953635.1	s__Alteromonas abrolhosensis	79.7742	327	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_000020585.3	s__Alteromonas mediterranea	79.7489	284	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_000808575.1	s__Alteromonas marina	79.7482	321	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_006538325.1	s__Alteromonas sp006538325	79.7104	296	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000172635.2	s__Alteromonas macleodii	79.6995	335	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_016405965.1	s__Alteromonas sp016405965	79.4835	286	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005117025.1	s__Alteromonas portus	79.4466	313	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	79.4149	319	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443615.1	s__Alteromonas sp003443615	79.3697	303	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002993325.1	s__Alteromonas gracilis	79.3237	302	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_001885075.1	s__Alteromonas sp001885075	79.2901	280	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811415.1	s__Alteromonas sp009811415	79.2217	299	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500895.1	s__Alteromonas genovensis	77.7107	193	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:32,610] [INFO] GTDB search result was written to OceanDNA-b34304/result_gtdb.tsv
[2023-03-16 04:06:32,611] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:32,612] [INFO] DFAST_QC result json was written to OceanDNA-b34304/dqc_result.json
[2023-03-16 04:06:32,612] [INFO] DFAST_QC completed!
[2023-03-16 04:06:32,612] [INFO] Total running time: 0h1m12s