[2023-03-15 05:51:32,071] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,071] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stg2d66afb6-c0d4-4412-92f8-b495d9bdc629/OceanDNA-b6759.fa | prodigal -d OceanDNA-b6759/cds.fna -a OceanDNA-b6759/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:58,395] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:58,395] [INFO] Task started: HMMsearch
[2023-03-15 05:51:58,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b6759/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/reference_markers.hmm OceanDNA-b6759/protein.faa > /dev/null
[2023-03-15 05:51:58,619] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:58,620] [INFO] Found 6/6 markers.
[2023-03-15 05:51:58,650] [INFO] Query marker FASTA was written to OceanDNA-b6759/markers.fasta
[2023-03-15 05:51:58,651] [INFO] Task started: Blastn
[2023-03-15 05:51:58,652] [INFO] Running command: blastn -query OceanDNA-b6759/markers.fasta -db /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/reference_markers.fasta -out OceanDNA-b6759/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:59,280] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:59,285] [INFO] Selected 22 target genomes.
[2023-03-15 05:51:59,285] [INFO] Target genome list was writen to OceanDNA-b6759/target_genomes.txt
[2023-03-15 05:51:59,299] [INFO] Task started: fastANI
[2023-03-15 05:51:59,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d66afb6-c0d4-4412-92f8-b495d9bdc629/OceanDNA-b6759.fa --refList OceanDNA-b6759/target_genomes.txt --output OceanDNA-b6759/fastani_result.tsv --threads 1
[2023-03-15 05:52:15,496] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:15,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:15,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:15,509] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:15,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:52:15,510] [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
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	79.3971	479	1274	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.9718	501	1274	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.6955	471	1274	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.6935	468	1274	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.6906	487	1274	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.614	486	1274	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.6028	489	1274	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.5962	488	1274	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.5606	463	1274	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.5302	467	1274	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.4911	462	1274	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.4186	399	1274	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.2561	425	1274	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.9543	408	1274	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.9242	365	1274	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.9087	392	1274	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	77.8917	383	1274	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.8332	441	1274	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	77.3898	300	1274	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2989	225	1274	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.2371	222	1274	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.1706	235	1274	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:15,510] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6759/tc_result.tsv
[2023-03-15 05:52:15,511] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:15,511] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:15,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/checkm_data
[2023-03-15 05:52:15,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:15,523] [INFO] Task started: CheckM
[2023-03-15 05:52:15,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6759/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6759/checkm_input OceanDNA-b6759/checkm_result
[2023-03-15 05:53:17,366] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:17,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:17,377] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:17,377] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:17,377] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6759/markers.fasta)
[2023-03-15 05:53:17,379] [INFO] Task started: Blastn
[2023-03-15 05:53:17,379] [INFO] Running command: blastn -query OceanDNA-b6759/markers.fasta -db /var/lib/cwl/stg7e9962fa-429d-4112-af13-a28fde190581/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6759/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:18,309] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:18,313] [INFO] Selected 20 target genomes.
[2023-03-15 05:53:18,313] [INFO] Target genome list was writen to OceanDNA-b6759/target_genomes_gtdb.txt
[2023-03-15 05:53:18,328] [INFO] Task started: fastANI
[2023-03-15 05:53:18,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d66afb6-c0d4-4412-92f8-b495d9bdc629/OceanDNA-b6759.fa --refList OceanDNA-b6759/target_genomes_gtdb.txt --output OceanDNA-b6759/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:33,127] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:33,138] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:53:33,138] [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_900114265.1	s__Flaviramulus basaltis	79.6004	552	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	79.3915	480	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.3571	554	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	79.0534	432	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.976	500	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.9012	405	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.7784	460	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.6877	468	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.6675	489	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.6072	436	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.595	490	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017814435.1	s__Mariniflexile gromovii	78.5345	457	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	78.4146	400	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.3579	412	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	78.3095	442	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.1818	361	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	77.9499	398	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.9484	410	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.9178	391	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:33,141] [INFO] GTDB search result was written to OceanDNA-b6759/result_gtdb.tsv
[2023-03-15 05:53:33,144] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:33,148] [INFO] DFAST_QC result json was written to OceanDNA-b6759/dqc_result.json
[2023-03-15 05:53:33,148] [INFO] DFAST_QC completed!
[2023-03-15 05:53:33,148] [INFO] Total running time: 0h2m1s