[2023-03-17 11:08:00,269] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference
[2023-03-17 11:08:01,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,431] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,431] [INFO] Running command: cat /var/lib/cwl/stgd3eba2ab-59a5-422e-96ab-c93087cb7eab/OceanDNA-b32230.fa | prodigal -d OceanDNA-b32230/cds.fna -a OceanDNA-b32230/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:15,491] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:15,491] [INFO] Task started: HMMsearch
[2023-03-17 11:08:15,491] [INFO] Running command: hmmsearch --tblout OceanDNA-b32230/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/reference_markers.hmm OceanDNA-b32230/protein.faa > /dev/null
[2023-03-17 11:08:15,685] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:15,686] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3eba2ab-59a5-422e-96ab-c93087cb7eab/OceanDNA-b32230.fa]
[2023-03-17 11:08:15,719] [INFO] Query marker FASTA was written to OceanDNA-b32230/markers.fasta
[2023-03-17 11:08:15,720] [INFO] Task started: Blastn
[2023-03-17 11:08:15,720] [INFO] Running command: blastn -query OceanDNA-b32230/markers.fasta -db /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/reference_markers.fasta -out OceanDNA-b32230/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:16,439] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:16,447] [INFO] Selected 20 target genomes.
[2023-03-17 11:08:16,447] [INFO] Target genome list was writen to OceanDNA-b32230/target_genomes.txt
[2023-03-17 11:08:16,463] [INFO] Task started: fastANI
[2023-03-17 11:08:16,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3eba2ab-59a5-422e-96ab-c93087cb7eab/OceanDNA-b32230.fa --refList OceanDNA-b32230/target_genomes.txt --output OceanDNA-b32230/fastani_result.tsv --threads 1
[2023-03-17 11:08:29,563] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:29,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:29,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:29,575] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:29,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:29,575] [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	82.4126	536	754	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.2341	318	754	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.5842	234	754	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.4511	254	754	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.3635	226	754	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.2592	164	754	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	77.2032	169	754	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	77.1964	154	754	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.1695	164	754	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.0071	132	754	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	76.9615	121	754	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	76.8726	158	754	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.8057	138	754	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	76.7469	165	754	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	76.6915	177	754	95	below_threshold
Sphingobium boeckii	strain=DSM 25079	GCA_014199215.1	1082345	1082345	type	True	76.6832	149	754	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	76.6322	143	754	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	76.5849	118	754	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	76.5722	137	754	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	76.4438	86	754	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:29,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32230/tc_result.tsv
[2023-03-17 11:08:29,580] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:29,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:29,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/checkm_data
[2023-03-17 11:08:29,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:29,589] [INFO] Task started: CheckM
[2023-03-17 11:08:29,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32230/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32230/checkm_input OceanDNA-b32230/checkm_result
[2023-03-17 11:09:07,742] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:07,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:07,799] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:07,799] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:07,800] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32230/markers.fasta)
[2023-03-17 11:09:07,801] [INFO] Task started: Blastn
[2023-03-17 11:09:07,801] [INFO] Running command: blastn -query OceanDNA-b32230/markers.fasta -db /var/lib/cwl/stg0f2cf19f-ad90-42fa-bb21-e9d0c389d809/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32230/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:09,067] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:09,078] [INFO] Selected 10 target genomes.
[2023-03-17 11:09:09,078] [INFO] Target genome list was writen to OceanDNA-b32230/target_genomes_gtdb.txt
[2023-03-17 11:09:09,164] [INFO] Task started: fastANI
[2023-03-17 11:09:09,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3eba2ab-59a5-422e-96ab-c93087cb7eab/OceanDNA-b32230.fa --refList OceanDNA-b32230/target_genomes_gtdb.txt --output OceanDNA-b32230/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:16,285] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:16,292] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:09:16,292] [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_002354635.1	s__Parasphingorhabdus sp002354635	85.6026	626	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	84.1248	499	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	83.7339	410	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	83.1489	572	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	83.0657	570	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	82.8642	571	754	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	82.5338	549	754	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	82.4163	536	754	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	82.3429	552	754	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	81.7771	455	754	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 11:09:16,296] [INFO] GTDB search result was written to OceanDNA-b32230/result_gtdb.tsv
[2023-03-17 11:09:16,304] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:16,311] [INFO] DFAST_QC result json was written to OceanDNA-b32230/dqc_result.json
[2023-03-17 11:09:16,311] [INFO] DFAST_QC completed!
[2023-03-17 11:09:16,311] [INFO] Total running time: 0h1m16s