[2023-03-16 08:10:35,104] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,112] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference
[2023-03-16 08:10:36,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,244] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,245] [INFO] Running command: cat /var/lib/cwl/stg96d69a06-69a4-4745-8113-ac8f2cf7c485/OceanDNA-b32606.fa | prodigal -d OceanDNA-b32606/cds.fna -a OceanDNA-b32606/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:11:08,016] [INFO] Task succeeded: Prodigal
[2023-03-16 08:11:08,016] [INFO] Task started: HMMsearch
[2023-03-16 08:11:08,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b32606/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/reference_markers.hmm OceanDNA-b32606/protein.faa > /dev/null
[2023-03-16 08:11:08,299] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:11:08,300] [INFO] Found 6/6 markers.
[2023-03-16 08:11:08,388] [INFO] Query marker FASTA was written to OceanDNA-b32606/markers.fasta
[2023-03-16 08:11:08,389] [INFO] Task started: Blastn
[2023-03-16 08:11:08,389] [INFO] Running command: blastn -query OceanDNA-b32606/markers.fasta -db /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/reference_markers.fasta -out OceanDNA-b32606/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:09,203] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:09,213] [INFO] Selected 28 target genomes.
[2023-03-16 08:11:09,213] [INFO] Target genome list was writen to OceanDNA-b32606/target_genomes.txt
[2023-03-16 08:11:09,228] [INFO] Task started: fastANI
[2023-03-16 08:11:09,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d69a06-69a4-4745-8113-ac8f2cf7c485/OceanDNA-b32606.fa --refList OceanDNA-b32606/target_genomes.txt --output OceanDNA-b32606/fastani_result.tsv --threads 1
[2023-03-16 08:11:33,900] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:33,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:33,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:33,915] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:33,915] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:11:33,916] [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
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	83.151	1145	1725	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	76.7168	310	1725	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.7073	312	1725	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.6951	426	1725	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.6039	259	1725	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5857	184	1725	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.5558	235	1725	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.4798	354	1725	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4646	388	1725	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4301	406	1725	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4251	408	1725	95	below_threshold
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	76.3889	317	1725	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2902	325	1725	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.2793	403	1725	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.277	283	1725	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	76.2106	259	1725	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.1509	279	1725	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.1181	247	1725	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	76.1	279	1725	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.0712	333	1725	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9524	363	1725	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	75.9094	278	1725	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.8742	273	1725	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	75.8137	194	1725	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.7131	248	1725	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.6487	189	1725	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	75.4451	156	1725	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	75.4158	194	1725	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:11:33,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32606/tc_result.tsv
[2023-03-16 08:11:33,925] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:33,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:33,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/checkm_data
[2023-03-16 08:11:33,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:33,940] [INFO] Task started: CheckM
[2023-03-16 08:11:33,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32606/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32606/checkm_input OceanDNA-b32606/checkm_result
[2023-03-16 08:13:04,407] [INFO] Task succeeded: CheckM
[2023-03-16 08:13:04,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:13:04,511] [INFO] ===== Completeness check finished =====
[2023-03-16 08:13:04,511] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:13:04,511] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32606/markers.fasta)
[2023-03-16 08:13:04,512] [INFO] Task started: Blastn
[2023-03-16 08:13:04,512] [INFO] Running command: blastn -query OceanDNA-b32606/markers.fasta -db /var/lib/cwl/stg15714d22-52dd-44bb-8823-c4767986d348/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32606/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:13:05,956] [INFO] Task succeeded: Blastn
[2023-03-16 08:13:05,988] [INFO] Selected 23 target genomes.
[2023-03-16 08:13:05,988] [INFO] Target genome list was writen to OceanDNA-b32606/target_genomes_gtdb.txt
[2023-03-16 08:13:06,029] [INFO] Task started: fastANI
[2023-03-16 08:13:06,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d69a06-69a4-4745-8113-ac8f2cf7c485/OceanDNA-b32606.fa --refList OceanDNA-b32606/target_genomes_gtdb.txt --output OceanDNA-b32606/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:13:25,845] [INFO] Task succeeded: fastANI
[2023-03-16 08:13:25,858] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:13:25,858] [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_000264455.2	s__Tistrella mobilis	96.0865	1594	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	conclusive
GCF_014636235.1	s__Tistrella bauzanensis	83.1617	1144	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.6789	411	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.4573	388	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	76.4239	177	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427665.1	s__Geminicoccus roseus	76.3825	318	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	76.3777	420	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	76.2996	192	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCA_009909005.1	s__JAAAOG01 sp009909005	76.2922	244	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JAAAOG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.2914	219	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.283	405	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856295.1	s__CAIZDL01 sp903856295	76.2684	198	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__CAIZDL01	95.0	99.95	99.95	0.95	0.95	2	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	76.1533	279	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.0978	329	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000526315.1	s__Methylopila sp000526315	76.0548	209	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.9681	255	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_008386565.1	s__Roseomonas oryzae	75.9213	274	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.8601	312	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.8139	201	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908425.1	s__JAAAPF01 sp009908425	75.7134	190	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693835.1	s__Rubrimonas sp007693835	75.6412	194	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501105.1	s__UBA7887 sp002501105	75.6389	55	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__UBA7887	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843125.1	s__CAIMOR01 sp903843125	75.5076	303	1725	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIMOR01	95.0	99.35	99.29	0.86	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-16 08:13:25,863] [INFO] GTDB search result was written to OceanDNA-b32606/result_gtdb.tsv
[2023-03-16 08:13:25,875] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:13:25,880] [INFO] DFAST_QC result json was written to OceanDNA-b32606/dqc_result.json
[2023-03-16 08:13:25,880] [INFO] DFAST_QC completed!
[2023-03-16 08:13:25,880] [INFO] Total running time: 0h2m51s