[2023-03-14 11:36:02,659] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,407] [INFO] Running command: cat /var/lib/cwl/stg11ac0513-8bdc-4edd-81b5-c098ea6c542a/OceanDNA-b38961.fa | prodigal -d OceanDNA-b38961/cds.fna -a OceanDNA-b38961/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:30,398] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:30,399] [INFO] Task started: HMMsearch
[2023-03-14 11:36:30,399] [INFO] Running command: hmmsearch --tblout OceanDNA-b38961/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/reference_markers.hmm OceanDNA-b38961/protein.faa > /dev/null
[2023-03-14 11:36:30,633] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:30,634] [INFO] Found 6/6 markers.
[2023-03-14 11:36:30,660] [INFO] Query marker FASTA was written to OceanDNA-b38961/markers.fasta
[2023-03-14 11:36:30,662] [INFO] Task started: Blastn
[2023-03-14 11:36:30,662] [INFO] Running command: blastn -query OceanDNA-b38961/markers.fasta -db /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/reference_markers.fasta -out OceanDNA-b38961/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:31,400] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:31,400] [INFO] Selected 15 target genomes.
[2023-03-14 11:36:31,401] [INFO] Target genome list was writen to OceanDNA-b38961/target_genomes.txt
[2023-03-14 11:36:31,410] [INFO] Task started: fastANI
[2023-03-14 11:36:31,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg11ac0513-8bdc-4edd-81b5-c098ea6c542a/OceanDNA-b38961.fa --refList OceanDNA-b38961/target_genomes.txt --output OceanDNA-b38961/fastani_result.tsv --threads 1
[2023-03-14 11:36:43,933] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:43,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:43,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:43,943] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 11:36:43,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:36:43,943] [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
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	99.0834	1317	1398	95	conclusive
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	83.9493	919	1398	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	81.6326	825	1398	95	below_threshold
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	81.047	796	1398	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.8886	506	1398	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.745	394	1398	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	78.6731	310	1398	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.5458	440	1398	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.5229	432	1398	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.3135	395	1398	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	78.2388	400	1398	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	78.114	377	1398	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	77.9145	325	1398	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.4869	250	1398	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.1938	63	1398	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:36:43,943] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38961/tc_result.tsv
[2023-03-14 11:36:43,943] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:43,943] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:43,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/checkm_data
[2023-03-14 11:36:43,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:43,949] [INFO] Task started: CheckM
[2023-03-14 11:36:43,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38961/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38961/checkm_input OceanDNA-b38961/checkm_result
[2023-03-14 11:37:48,859] [INFO] Task succeeded: CheckM
[2023-03-14 11:37:48,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:37:48,869] [INFO] ===== Completeness check finished =====
[2023-03-14 11:37:48,869] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:37:48,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38961/markers.fasta)
[2023-03-14 11:37:48,871] [INFO] Task started: Blastn
[2023-03-14 11:37:48,871] [INFO] Running command: blastn -query OceanDNA-b38961/markers.fasta -db /var/lib/cwl/stg664bdd34-6581-434a-98c9-6ea1d102379a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38961/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:37:50,121] [INFO] Task succeeded: Blastn
[2023-03-14 11:37:50,122] [INFO] Selected 12 target genomes.
[2023-03-14 11:37:50,122] [INFO] Target genome list was writen to OceanDNA-b38961/target_genomes_gtdb.txt
[2023-03-14 11:37:50,199] [INFO] Task started: fastANI
[2023-03-14 11:37:50,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg11ac0513-8bdc-4edd-81b5-c098ea6c542a/OceanDNA-b38961.fa --refList OceanDNA-b38961/target_genomes_gtdb.txt --output OceanDNA-b38961/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:38:00,886] [INFO] Task succeeded: fastANI
[2023-03-14 11:38:00,893] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:38:00,893] [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_007671675.1	s__Marinobacter maritimus	99.0834	1317	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	conclusive
GCA_018066865.1	s__Marinobacter sp018066865	90.0924	930	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.94	99.94	0.89	0.89	2	-
GCF_900142385.1	s__Marinobacter antarcticus	83.9355	921	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001858325.1	s__Marinobacter sp001858325	82.4576	914	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.26	95.26	0.85	0.85	2	-
GCF_002407605.1	s__Marinobacter sp002407605	81.6484	872	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806975.1	s__Marinobacter aromaticivorans	81.643	825	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215155.1	s__Marinobacter sp900215155	81.5749	860	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.10	97.17	0.88	0.86	3	-
GCF_016597815.1	s__Marinobacter sp016597815	81.5535	804	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
GCA_011049865.1	s__Marinobacter antarcticus_A	81.5273	794	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318275.1	s__Marinobacter sp003318275	81.2715	699	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806945.1	s__Marinobacter salexigens	81.0552	795	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597725.1	s__Marinobacter sp016597725	81.0552	787	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:38:00,983] [INFO] GTDB search result was written to OceanDNA-b38961/result_gtdb.tsv
[2023-03-14 11:38:00,984] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:38:00,987] [INFO] DFAST_QC result json was written to OceanDNA-b38961/dqc_result.json
[2023-03-14 11:38:00,987] [INFO] DFAST_QC completed!
[2023-03-14 11:38:00,987] [INFO] Total running time: 0h1m58s