[2023-06-07 19:05:15,437] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:15,483] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:15,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference
[2023-06-07 19:05:17,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:17,199] [INFO] Task started: Prodigal
[2023-06-07 19:05:17,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg01abe150-69e6-453c-b71e-c7a1766841a0/GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:23,344] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:23,345] [INFO] Task started: HMMsearch
[2023-06-07 19:05:23,345] [INFO] Running command: hmmsearch --tblout GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/reference_markers.hmm GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:23,615] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:23,617] [INFO] Found 6/6 markers.
[2023-06-07 19:05:23,651] [INFO] Query marker FASTA was written to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 19:05:23,652] [INFO] Task started: Blastn
[2023-06-07 19:05:23,652] [INFO] Running command: blastn -query GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/reference_markers.fasta -out GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:24,309] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:24,313] [INFO] Selected 35 target genomes.
[2023-06-07 19:05:24,313] [INFO] Target genome list was writen to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 19:05:24,317] [INFO] Task started: fastANI
[2023-06-07 19:05:24,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg01abe150-69e6-453c-b71e-c7a1766841a0/GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:53,049] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:53,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:53,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:53,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:53,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:05:53,052] [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
--------------------------------------------------------------------------------
[2023-06-07 19:05:53,054] [INFO] DFAST Taxonomy check result was written to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 19:05:53,054] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:53,055] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:53,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/checkm_data
[2023-06-07 19:05:53,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:53,090] [INFO] Task started: CheckM
[2023-06-07 19:05:53,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 19:06:17,679] [INFO] Task succeeded: CheckM
[2023-06-07 19:06:17,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:06:17,701] [INFO] ===== Completeness check finished =====
[2023-06-07 19:06:17,701] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:06:17,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 19:06:17,702] [INFO] Task started: Blastn
[2023-06-07 19:06:17,702] [INFO] Running command: blastn -query GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c382276-1e80-4478-b7d0-a67cb461fb5c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:06:18,663] [INFO] Task succeeded: Blastn
[2023-06-07 19:06:18,667] [INFO] Selected 19 target genomes.
[2023-06-07 19:06:18,668] [INFO] Target genome list was writen to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:06:18,670] [INFO] Task started: fastANI
[2023-06-07 19:06:18,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg01abe150-69e6-453c-b71e-c7a1766841a0/GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:06:27,639] [INFO] Task succeeded: fastANI
[2023-06-07 19:06:27,664] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:06:27,664] [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_902788415.1	s__UBA1067 sp902788415	97.9646	487	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016303225.1	s__UBA1067 sp016303225	85.3532	354	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320855.1	s__UBA1067 sp900320855	81.3636	280	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002321305.1	s__UBA1067 sp002321305	81.2876	284	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463935.1	s__UBA1067 sp017463935	80.1363	195	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902770045.1	s__UBA1067 sp902770045	79.7937	214	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	95.51	95.51	0.70	0.70	2	-
GCA_902764415.1	s__UBA1067 sp002351765	79.7783	246	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.23	96.23	0.86	0.81	5	-
GCA_016284515.1	s__UBA1067 sp016284515	79.7001	252	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449695.1	s__UBA1067 sp002449695	79.6939	252	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800055.1	s__UBA1067 sp902800055	79.5341	232	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	96.21	96.21	0.84	0.84	3	-
GCA_902773015.1	s__UBA1067 sp902773015	79.519	239	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412325.1	s__UBA1067 sp017412325	79.5005	119	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799955.1	s__UBA1067 sp902799955	79.433	216	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	95.66	95.66	0.72	0.72	2	-
GCA_902761275.1	s__UBA1067 sp902761275	79.1247	195	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017403825.1	s__UBA1067 sp017403825	79.026	218	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799385.1	s__UBA1067 sp902799385	78.9179	211	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650345.1	s__UBA1067 sp017650345	78.662	170	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767325.1	s__UBA1067 sp900767325	78.5785	142	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315875.1	s__UBA1067 sp002315875	78.0135	181	720	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:06:27,667] [INFO] GTDB search result was written to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 19:06:27,667] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:06:27,671] [INFO] DFAST_QC result json was written to GCA_947367435.1_SRR15429281_bin.1_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 19:06:27,671] [INFO] DFAST_QC completed!
[2023-06-07 19:06:27,671] [INFO] Total running time: 0h1m12s