[2023-03-19 03:10:00,764] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference
[2023-03-19 03:10:01,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,901] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,901] [INFO] Running command: cat /var/lib/cwl/stgda7ca625-3b79-400a-bb61-57ba6e757c00/OceanDNA-b32143.fa | prodigal -d OceanDNA-b32143/cds.fna -a OceanDNA-b32143/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:12,389] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:12,390] [INFO] Task started: HMMsearch
[2023-03-19 03:10:12,390] [INFO] Running command: hmmsearch --tblout OceanDNA-b32143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/reference_markers.hmm OceanDNA-b32143/protein.faa > /dev/null
[2023-03-19 03:10:12,560] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:12,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda7ca625-3b79-400a-bb61-57ba6e757c00/OceanDNA-b32143.fa]
[2023-03-19 03:10:12,577] [INFO] Query marker FASTA was written to OceanDNA-b32143/markers.fasta
[2023-03-19 03:10:12,578] [INFO] Task started: Blastn
[2023-03-19 03:10:12,578] [INFO] Running command: blastn -query OceanDNA-b32143/markers.fasta -db /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/reference_markers.fasta -out OceanDNA-b32143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:13,306] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:13,306] [INFO] Selected 17 target genomes.
[2023-03-19 03:10:13,307] [INFO] Target genome list was writen to OceanDNA-b32143/target_genomes.txt
[2023-03-19 03:10:13,314] [INFO] Task started: fastANI
[2023-03-19 03:10:13,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7ca625-3b79-400a-bb61-57ba6e757c00/OceanDNA-b32143.fa --refList OceanDNA-b32143/target_genomes.txt --output OceanDNA-b32143/fastani_result.tsv --threads 1
[2023-03-19 03:10:23,166] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:23,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:23,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:23,177] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 03:10:23,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 03:10:23,177] [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
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	97.793	511	540	95	conclusive
Stakelama pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	97.7797	513	540	95	conclusive
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	82.2277	346	540	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.3616	242	540	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.835	238	540	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.8797	172	540	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	77.747	172	540	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	77.7379	187	540	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	77.4516	170	540	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.4252	172	540	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.3708	139	540	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.0687	54	540	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.058	154	540	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	76.7959	112	540	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.7337	149	540	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.6689	66	540	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	76.5583	54	540	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:10:23,177] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32143/tc_result.tsv
[2023-03-19 03:10:23,177] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:23,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:23,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/checkm_data
[2023-03-19 03:10:23,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:23,182] [INFO] Task started: CheckM
[2023-03-19 03:10:23,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32143/checkm_input OceanDNA-b32143/checkm_result
[2023-03-19 03:10:53,364] [INFO] Task succeeded: CheckM
[2023-03-19 03:10:53,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:10:53,367] [INFO] ===== Completeness check finished =====
[2023-03-19 03:10:53,367] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:10:53,367] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32143/markers.fasta)
[2023-03-19 03:10:53,367] [INFO] Task started: Blastn
[2023-03-19 03:10:53,367] [INFO] Running command: blastn -query OceanDNA-b32143/markers.fasta -db /var/lib/cwl/stg55481149-1140-4b16-a422-3267bbd16abc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:54,657] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:54,658] [INFO] Selected 27 target genomes.
[2023-03-19 03:10:54,658] [INFO] Target genome list was writen to OceanDNA-b32143/target_genomes_gtdb.txt
[2023-03-19 03:10:54,674] [INFO] Task started: fastANI
[2023-03-19 03:10:54,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7ca625-3b79-400a-bb61-57ba6e757c00/OceanDNA-b32143.fa --refList OceanDNA-b32143/target_genomes_gtdb.txt --output OceanDNA-b32143/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:11,509] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:11,524] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:11,524] [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_004361835.1	s__Sphingomonas pacifica	97.7797	513	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	conclusive
GCA_018122655.1	s__Sphingomonas sp018122655	80.3529	267	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199335.1	s__Sphingomonas sediminis	79.3524	243	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	78.9807	216	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171655.1	s__Sphingomonas portus	78.817	239	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	78.4953	233	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506605.1	s__Sphingomonas sp902506605	78.2329	192	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	77.9969	187	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_014334115.1	s__Sphingomonas sp014334115	77.9741	205	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.8735	173	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014489075.1	s__Sphingomonas sp014489075	77.8722	182	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	77.7986	198	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	77.7647	220	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	77.7471	172	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	77.7228	189	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003550065.1	s__Sphingomonas caeni	77.6619	192	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	77.6018	181	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003075315.1	s__Sphingomonas sp003075315	77.5903	167	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_000712135.1	s__Sphingomonas sp000712135	77.5577	202	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	77.4732	193	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427645.1	s__Sphingomonas phyllosphaerae	77.4696	169	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	77.4252	172	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	77.2996	169	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	77.2331	154	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	77.0497	83	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	76.782	59	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	76.5333	80	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:11,524] [INFO] GTDB search result was written to OceanDNA-b32143/result_gtdb.tsv
[2023-03-19 03:11:11,525] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:11,527] [INFO] DFAST_QC result json was written to OceanDNA-b32143/dqc_result.json
[2023-03-19 03:11:11,527] [INFO] DFAST_QC completed!
[2023-03-19 03:11:11,527] [INFO] Total running time: 0h1m11s