[2023-03-17 11:08:00,269] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference
[2023-03-17 11:08:01,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,419] [INFO] Running command: cat /var/lib/cwl/stg3b5c47b4-6579-456b-bee2-46ddd34d5e46/OceanDNA-b32281.fa | prodigal -d OceanDNA-b32281/cds.fna -a OceanDNA-b32281/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:21,559] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:21,560] [INFO] Task started: HMMsearch
[2023-03-17 11:08:21,560] [INFO] Running command: hmmsearch --tblout OceanDNA-b32281/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/reference_markers.hmm OceanDNA-b32281/protein.faa > /dev/null
[2023-03-17 11:08:21,769] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:21,770] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b5c47b4-6579-456b-bee2-46ddd34d5e46/OceanDNA-b32281.fa]
[2023-03-17 11:08:21,876] [INFO] Query marker FASTA was written to OceanDNA-b32281/markers.fasta
[2023-03-17 11:08:21,877] [INFO] Task started: Blastn
[2023-03-17 11:08:21,878] [INFO] Running command: blastn -query OceanDNA-b32281/markers.fasta -db /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/reference_markers.fasta -out OceanDNA-b32281/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:22,556] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:22,561] [INFO] Selected 15 target genomes.
[2023-03-17 11:08:22,561] [INFO] Target genome list was writen to OceanDNA-b32281/target_genomes.txt
[2023-03-17 11:08:22,569] [INFO] Task started: fastANI
[2023-03-17 11:08:22,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5c47b4-6579-456b-bee2-46ddd34d5e46/OceanDNA-b32281.fa --refList OceanDNA-b32281/target_genomes.txt --output OceanDNA-b32281/fastani_result.tsv --threads 1
[2023-03-17 11:08:31,742] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:31,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:31,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:31,752] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:31,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:31,752] [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	83.6021	733	1080	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.1369	386	1080	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.8853	360	1080	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.8828	328	1080	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.8813	321	1080	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.783	126	1080	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.5531	156	1080	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.5126	151	1080	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	76.4678	145	1080	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.45	106	1080	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.3462	127	1080	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	76.123	105	1080	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	76.1225	105	1080	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.1042	124	1080	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.0105	118	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:31,754] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32281/tc_result.tsv
[2023-03-17 11:08:31,757] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:31,757] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:31,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/checkm_data
[2023-03-17 11:08:31,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:31,766] [INFO] Task started: CheckM
[2023-03-17 11:08:31,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32281/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32281/checkm_input OceanDNA-b32281/checkm_result
[2023-03-17 11:09:23,211] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:23,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:23,318] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:23,318] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:23,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32281/markers.fasta)
[2023-03-17 11:09:23,319] [INFO] Task started: Blastn
[2023-03-17 11:09:23,319] [INFO] Running command: blastn -query OceanDNA-b32281/markers.fasta -db /var/lib/cwl/stg0f3d4c5c-e464-48d3-ae0f-c8e8142e8786/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32281/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:24,520] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:24,526] [INFO] Selected 10 target genomes.
[2023-03-17 11:09:24,526] [INFO] Target genome list was writen to OceanDNA-b32281/target_genomes_gtdb.txt
[2023-03-17 11:09:24,564] [INFO] Task started: fastANI
[2023-03-17 11:09:24,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5c47b4-6579-456b-bee2-46ddd34d5e46/OceanDNA-b32281.fa --refList OceanDNA-b32281/target_genomes_gtdb.txt --output OceanDNA-b32281/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:31,808] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:31,814] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:09:31,815] [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_002776575.1	s__Parasphingorhabdus sp002776575	86.1204	882	1080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	85.4759	798	1080	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	84.5453	806	1080	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	84.2165	835	1080	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	83.9308	608	1080	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	83.6021	733	1080	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	83.521	480	1080	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	83.2512	445	1080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	82.6807	725	1080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	81.9501	678	1080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:31,817] [INFO] GTDB search result was written to OceanDNA-b32281/result_gtdb.tsv
[2023-03-17 11:09:31,820] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:31,826] [INFO] DFAST_QC result json was written to OceanDNA-b32281/dqc_result.json
[2023-03-17 11:09:31,826] [INFO] DFAST_QC completed!
[2023-03-17 11:09:31,826] [INFO] Total running time: 0h1m32s