[2023-03-16 10:13:35,985] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:13:35,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:13:35,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference
[2023-03-16 10:13:37,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:13:37,157] [INFO] Task started: Prodigal
[2023-03-16 10:13:37,157] [INFO] Running command: cat /var/lib/cwl/stg0223707a-8056-46f9-b31a-bb70637f353e/OceanDNA-b32289.fa | prodigal -d OceanDNA-b32289/cds.fna -a OceanDNA-b32289/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:13:55,846] [INFO] Task succeeded: Prodigal
[2023-03-16 10:13:55,846] [INFO] Task started: HMMsearch
[2023-03-16 10:13:55,846] [INFO] Running command: hmmsearch --tblout OceanDNA-b32289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/reference_markers.hmm OceanDNA-b32289/protein.faa > /dev/null
[2023-03-16 10:13:56,049] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:13:56,049] [INFO] Found 6/6 markers.
[2023-03-16 10:13:56,070] [INFO] Query marker FASTA was written to OceanDNA-b32289/markers.fasta
[2023-03-16 10:13:56,071] [INFO] Task started: Blastn
[2023-03-16 10:13:56,071] [INFO] Running command: blastn -query OceanDNA-b32289/markers.fasta -db /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/reference_markers.fasta -out OceanDNA-b32289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:13:56,847] [INFO] Task succeeded: Blastn
[2023-03-16 10:13:56,848] [INFO] Selected 18 target genomes.
[2023-03-16 10:13:56,848] [INFO] Target genome list was writen to OceanDNA-b32289/target_genomes.txt
[2023-03-16 10:13:56,860] [INFO] Task started: fastANI
[2023-03-16 10:13:56,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg0223707a-8056-46f9-b31a-bb70637f353e/OceanDNA-b32289.fa --refList OceanDNA-b32289/target_genomes.txt --output OceanDNA-b32289/fastani_result.tsv --threads 1
[2023-03-16 10:14:08,195] [INFO] Task succeeded: fastANI
[2023-03-16 10:14:08,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:14:08,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:14:08,206] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:14:08,206] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:14:08,206] [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	82.7437	699	999	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.5713	402	999	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.1726	324	999	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.9751	289	999	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.9589	308	999	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	77.4394	161	999	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.062	166	999	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.0525	176	999	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	76.992	172	999	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.8226	186	999	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	76.7508	144	999	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	76.6723	159	999	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.6445	145	999	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	76.6311	126	999	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	76.518	111	999	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.5035	141	999	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	76.1648	111	999	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	76.1648	111	999	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:14:08,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32289/tc_result.tsv
[2023-03-16 10:14:08,207] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:14:08,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:14:08,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/checkm_data
[2023-03-16 10:14:08,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:14:08,238] [INFO] Task started: CheckM
[2023-03-16 10:14:08,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32289/checkm_input OceanDNA-b32289/checkm_result
[2023-03-16 10:14:58,083] [INFO] Task succeeded: CheckM
[2023-03-16 10:14:58,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:14:58,088] [INFO] ===== Completeness check finished =====
[2023-03-16 10:14:58,088] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:14:58,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32289/markers.fasta)
[2023-03-16 10:14:58,113] [INFO] Task started: Blastn
[2023-03-16 10:14:58,113] [INFO] Running command: blastn -query OceanDNA-b32289/markers.fasta -db /var/lib/cwl/stg86e411e9-18e9-4091-a23e-4ab79d64ed10/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:14:59,703] [INFO] Task succeeded: Blastn
[2023-03-16 10:14:59,705] [INFO] Selected 12 target genomes.
[2023-03-16 10:14:59,705] [INFO] Target genome list was writen to OceanDNA-b32289/target_genomes_gtdb.txt
[2023-03-16 10:14:59,744] [INFO] Task started: fastANI
[2023-03-16 10:14:59,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg0223707a-8056-46f9-b31a-bb70637f353e/OceanDNA-b32289.fa --refList OceanDNA-b32289/target_genomes_gtdb.txt --output OceanDNA-b32289/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:15:08,911] [INFO] Task succeeded: fastANI
[2023-03-16 10:15:08,918] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:15:08,919] [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	99.9085	992	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018067055.1	s__Parasphingorhabdus sp018067055	84.7005	470	999	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	84.0601	585	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	83.1986	702	999	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	83.1419	737	999	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	82.9978	704	999	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	82.7437	699	999	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	82.6895	709	999	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	82.1092	550	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598415.1	s__Sphingomonas mali	76.6583	160	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	76.6356	125	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:15:08,919] [INFO] GTDB search result was written to OceanDNA-b32289/result_gtdb.tsv
[2023-03-16 10:15:08,920] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:15:08,922] [INFO] DFAST_QC result json was written to OceanDNA-b32289/dqc_result.json
[2023-03-16 10:15:08,922] [INFO] DFAST_QC completed!
[2023-03-16 10:15:08,922] [INFO] Total running time: 0h1m33s